HCV protease inhibitors and uses thereof

ABSTRACT

The present invention provides compounds, pharmaceutically acceptable compositions thereof, and methods of using the same.

CROSS REFERENCE TO RELATED APPLICATIONS

The present application is a divisional of U.S. patent application Ser. No. 14/010,892, filed Aug. 27, 2013, now U.S. Pat. No. 8,980,935, which is a divisional of U.S. patent application Ser. No. 13/443,847, filed Apr. 10, 2012, now U.S. Pat. No. 8,524,760, which is a divisional of U.S. patent application Ser. No. 12/541,347, filed Aug. 14, 2009, now U.S. Pat. No. 8,188,137, which claims priority to U.S. provisional application Ser. No. 61/089,269, filed Aug. 15, 2008, and U.S. provisional application Ser. No. 61/098,662, filed Sep. 19, 2008, the entirety of each of which is hereby incorporated by reference.

TECHNICAL FIELD OF THE INVENTION

The present invention relates to compounds useful as inhibitors of HCV protease. The invention also provides pharmaceutically acceptable compositions comprising compounds of the present invention and methods of using said compositions in the treatment of various disorders.

In accordance with 37 CFR 1.52(e)(5), a Sequence Listing in the form of a text file (entitled “Sequence Listing.txt,” created on Apr. 10, 2012, and 19 kilobytes) is incorporated herein by reference in its entirety.

BACKGROUND OF THE INVENTION

It is estimated that over 170 million people worldwide are infected with the Hepatitis C virus (HCV). With an estimated human sero-prevalence of 3% globally, HCV is the major cause for most cases of non-A, non-B hepatitis, (Alberti, A. et al., J. Hepatology 31., (Suppl. 1): 17-24, 1999). While the symptoms of acute hepatitis subside in some patients, at least 85% of HCV infections become chronic, and 20% of those infected develop liver cirrhosis. There is less than a 50% survival rate at four years post cirrhosis diagnosis. Chronic HCV infection is also associated with increased incidence of hepatocellular carcinoma.

HCV is a positive-stranded RNA virus whose genome encodes a polyprotein of approximately 3000 amino acids. This precursor protein is processed into at least 10 viral structural and nonstructural proteins: C, E1, E2, p7, NS2, NS3, NS4A, NS4B, NS5A, and NS5B (Blight, K. J., et al., Antiviral Ther. 3, Suppl. 3: 71-81, 1998). HCV nonstructural (NS) proteins are derived by proteolytic cleavage of the polyprotein and are presumed to provide the essential catalytic machinery for viral replication.

NS3 is an approximately 68 Kda protein, and has both an N-terminal serine protease domain and an RNA-dependent ATPase domain at its C-terminus. It has been shown that the NS4A protein serves as a co-factor for the serine protease activity of NS3. NS3 functions as a proteolytic enzyme that cleaves sites liberating other nonstructural proteins necessary for HCV replication and is a viable therapeutic target for antiviral chemotherapy.

No vaccines are available for HCV, and the established therapy of interferon treatment is effective in only 15-20% of patients (Weiland, O., FEMS Microbiol. Rev. 14: 279-88, 1994), and has significant side effects (Walker, M. A., et al., DDT 4: 518-29, 1999; Moradpour, D., et al., Eur. J. Gastroenterol. Hepatol. 11: 1199-1202, 1999). While the current standard of care, pegylated interferon α in combination with ribavirin, is more efficacious and appears to decrease hepatocellular carcinoma in patients with HCV-related cirrhosis (Hung, C. H., et al., J Viral Hepatitis 13(6): 409-414, 2006), this treatment has also been shown to produce side effects such as thyroid dysfunction (Huang, J. F., et al., J Viral Hepatitis 13(6): 396-401, 2006).

The poor prognosis for patients suffering from HCV infection and the current lack of effective, approved treatments, highlights the overwhelming need for new inhibitors of HCV NS3 protease.

SUMMARY OF THE INVENTION

It has now been found that compounds of this invention, and pharmaceutically acceptable compositions thereof, are effective as inhibitors of HCV protease. Such compounds have the general formula I:

or a pharmaceutically acceptable salt thereof, wherein R¹, R², R³, R⁴, R^(a), R^(b), R^(x) and R^(y) are as defined herein.

Compounds of the present invention, and pharmaceutically acceptable compositions thereof, are useful for treating a variety of diseases, disorders or conditions, associated with HCV. Such diseases, disorders, or conditions include those described herein.

Compounds provided by this invention are also useful for the study of HCV protease in biological and pathological phenomena; the study of intracellular signal transduction pathways mediated by HCV protease; and the comparative evaluation of new HCV protease inhibitors.

BRIEF DESCRIPTION OF THE DRAWINGS

FIG. 1 depicts a mass spectroscopic analysis of HCV NS3/4A wild-type protease alone and in the presence of test compound I-1 (upper panel), and HCV NS3/4A mutant C159S protease in the presence of test compound I-1 (lower panel).

FIG. 2 depicts a mass spectroscopic analysis of HCV NS3/4A wild-type protease in the presence of test compound I-11.

FIG. 3 depicts a mass spectroscopic analysis of HCV NS3/4A wild-type protease alone (upper panel) and in the presence of telaprevir (lower panel).

DETAILED DESCRIPTION OF CERTAIN EMBODIMENTS 1. General Description of Compounds of the Invention

In certain embodiments, the present invention provides a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

-   one of R^(a) and R^(b) is hydrogen and the other is —OH or —OC(O)R′,     or R^(a) and R^(b) are taken together to form an oxo group; -   R′ is an optionally substituted group selected from C₁₋₆ aliphatic,     C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered heteroaryl having     1-4 heteroatoms independently selected from nitrogen, oxygen, or     sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R^(x) and R^(y) are taken together to form an optionally substituted     C₃₋₇ membered ring having 0-2 heteroatoms independently selected     from nitrogen, oxygen, or sulfur; -   R¹ is an optionally substituted group selected from C₁₋₆ aliphatic     or C₃₋₇ cycloalkyl(C₁₋₃ alkyl); -   R² is hydrogen or an optionally substituted group selected from C₁₋₆     aliphatic or C₃₋₇ cycloalkyl; -   R³ is a warhead group; -   R⁴ is —NHC(O)NHR⁵, —NHC(O)OR⁶, or

-   R⁵ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R⁶ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R⁷ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R is hydrogen or an optionally substituted group selected from C₁₋₆     aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered     heteroaryl having 1-4 heteroatoms independently selected from     nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2     heteroatoms independently selected from nitrogen, oxygen, or sulfur.

2. Compounds and Definitions

Compounds of this invention include those described generally above, and are further illustrated by the classes, subclasses, and species disclosed herein. As used herein, the following definitions shall apply unless otherwise indicated. For purposes of this invention, the chemical elements are identified in accordance with the Periodic Table of the Elements, CAS version, Handbook of Chemistry and Physics, 75^(th) Ed. Additionally, general principles of organic chemistry are described in “Organic Chemistry”, Thomas Sorrell, University Science Books, Sausalito: 1999, and “March's Advanced Organic Chemistry”, 5^(th) Ed., Ed.: Smith, M. B. and March, J., John Wiley & Sons, New York: 2001, the entire contents of which are hereby incorporated by reference.

The term “aliphatic” or “aliphatic group”, as used herein, means a straight-chain (i.e., unbranched) or branched, substituted or unsubstituted hydrocarbon chain that is completely saturated or that contains one or more units of unsaturation, or a monocyclic hydrocarbon or bicyclic hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic (also referred to herein as “carbocycle,” “cycloaliphatic” or “cycloalkyl”), that has a single point of attachment to the rest of the molecule. Unless otherwise specified, aliphatic groups contain 1-6 aliphatic carbon atoms. In some embodiments, aliphatic groups contain 1-5 aliphatic carbon atoms. In other embodiments, aliphatic groups contain 1-4 aliphatic carbon atoms. In still other embodiments, aliphatic groups contain 1-3 aliphatic carbon atoms, and in yet other embodiments, aliphatic groups contain 1-2 aliphatic carbon atoms. In some embodiments, “cycloaliphatic” (or “carbocycle” or “cycloalkyl”) refers to a monocyclic C₃-C₆ hydrocarbon that is completely saturated or that contains one or more units of unsaturation, but which is not aromatic, that has a single point of attachment to the rest of the molecule. Suitable aliphatic groups include, but are not limited to, linear or branched, substituted or unsubstituted alkyl, alkenyl, alkynyl groups and hybrids thereof such as (cycloalkyl)alkyl, (cycloalkenyl)alkyl or (cycloalkyl)alkenyl.

As used herein, the term “bridged bicyclic” refers to any bicyclic ring system, i.e. carbocyclic or heterocyclic, saturated or partially unsaturated, having at least one bridge. As defined by IUPAC, a “bridge” is an unbranched chain of atoms or an atom or a valence bond connecting two bridgeheads, where a “bridgehead” is any skeletal atom of the ring system which is bonded to three or more skeletal atoms (excluding hydrogen). In some embodiments, a bridged bicyclic group has 7-12 ring members and 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Such bridged bicyclic groups are well known in the art and include those groups set forth below where each group is attached to the rest of the molecule at any substitutable carbon or nitrogen atom. Unless otherwise specified, a bridged bicyclic group is optionally substituted with one or more substituents as set forth for aliphatic groups. Additionally or alternatively, any substitutable nitrogen of a bridged bicyclic group is optionally substituted. Exemplary bridged bicyclics include:

The term “lower alkyl” refers to a C₁₋₄ straight or branched alkyl group. Exemplary lower alkyl groups are methyl, ethyl, propyl, isopropyl, butyl, isobutyl, and tert-butyl.

The term “lower haloalkyl” refers to a C₁₋₄ straight or branched alkyl group that is substituted with one or more halogen atoms.

The term “heteroatom” means one or more of oxygen, sulfur, nitrogen, phosphorus, or silicon (including, any oxidized form of nitrogen, sulfur, phosphorus, or silicon; the quaternized form of any basic nitrogen or; a substitutable nitrogen of a heterocyclic ring, for example N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl) or NR′ (as in N-substituted pyrrolidinyl)).

The term “unsaturated,” as used herein, means that a moiety has one or more units of unsaturation.

As used herein, the term “bivalent C₁₋₈ (or C₁₋₆, C₂₋₈, C₂₋₆) saturated or unsaturated, straight or branched, hydrocarbon chain”, refers to bivalent alkylene, alkenylene, and alkynylene chains that are straight or branched as defined herein.

The term “alkylene” refers to a bivalent alkyl group. An “alkylene chain” is a polymethylene group, i.e., —(CH₂)_(n)—, wherein n is a positive integer from 1 to 8, from 1 to 6, from 1 to 4, from 1 to 3, from 1 to 2, from 2 to 8, from 2 to 6, or from 2 to 3. A substituted alkylene chain is a polymethylene group in which one or more methylene hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.

The term “alkenylene” refers to a bivalent alkenyl group. A substituted alkenylene chain is a polymethylene group containing at least one double bond in which one or more hydrogen atoms are replaced with a substituent. Suitable substituents include those described below for a substituted aliphatic group.

As used herein, the term “cyclopropylenyl” refers to a bivalent cyclopropyl group of the following structure:

The term “halogen” means F, Cl, Br, or I.

The term “aryl” used alone or as part of a larger moiety as in “aralkyl,” “aralkoxy,” or “aryloxyalkyl,” refers to monocyclic or bicyclic ring systems having a total of five to fourteen ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains 3 to 7 ring members. The term “aryl” may be used interchangeably with the term “aryl ring.”

The term “aryl” used alone or as part of a larger moiety as in “aralkyl,” “aralkoxy,” or “aryloxyalkyl,” refers to monocyclic and bicyclic ring systems having a total of five to 10 ring members, wherein at least one ring in the system is aromatic and wherein each ring in the system contains three to seven ring members. The term “aryl” may be used interchangeably with the term “aryl ring”. In certain embodiments of the present invention, “aryl” refers to an aromatic ring system which includes, but not limited to, phenyl, biphenyl, naphthyl, anthracyl and the like, which may bear one or more substituents. Also included within the scope of the term “aryl,” as it is used herein, is a group in which an aromatic ring is fused to one or more non-aromatic rings, such as indanyl, phthalimidyl, naphthimidyl, phenanthridinyl, or tetrahydronaphthyl, and the like.

The terms “heteroaryl” and “heteroar-,” used alone or as part of a larger moiety, e.g., “heteroaralkyl,” or “heteroaralkoxy,” refer to groups having 5 to 10 ring atoms, preferably 5, 6, or 9 ring atoms; having 6, 10, or 14π electrons shared in a cyclic array; and having, in addition to carbon atoms, from one to five heteroatoms. The term “heteroatom” refers to nitrogen, oxygen, or sulfur, and includes any oxidized form of nitrogen or sulfur, and any quaternized form of a basic nitrogen. Heteroaryl groups include, without limitation, thienyl, furanyl, pyrrolyl, imidazolyl, pyrazolyl, triazolyl, tetrazolyl, oxazolyl, isoxazolyl, oxadiazolyl, thiazolyl, isothiazolyl, thiadiazolyl, pyridyl, pyridazinyl, pyrimidinyl, pyrazinyl, indolizinyl, purinyl, naphthyridinyl, and pteridinyl. The terms “heteroaryl” and “heteroar-”, as used herein, also include groups in which a heteroaromatic ring is fused to one or more aryl, cycloaliphatic, or heterocyclyl rings, where the radical or point of attachment is on the heteroaromatic ring. Nonlimiting examples include indolyl, isoindolyl, benzothienyl, benzofuranyl, dibenzofuranyl, indazolyl, benzimidazolyl, benzthiazolyl, quinolyl, isoquinolyl, cinnolinyl, phthalazinyl, quinazolinyl, quinoxalinyl, 4H-quinolizinyl, carbazolyl, acridinyl, phenazinyl, phenothiazinyl, phenoxazinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, and pyrido[2,3-b]-1,4-oxazin-3(4H)-one. A heteroaryl group may be mono- or bicyclic. The term “heteroaryl” may be used interchangeably with the terms “heteroaryl ring,” “heteroaryl group,” or “heteroaromatic,” any of which terms include rings that are optionally substituted. The term “heteroaralkyl” refers to an alkyl group substituted by a heteroaryl, wherein the alkyl and heteroaryl portions independently are optionally substituted.

As used herein, the terms “heterocycle,” “heterocyclyl,” “heterocyclic radical,” and “heterocyclic ring” are used interchangeably and refer to a stable 5- to 7-membered monocyclic or 7-10-membered bicyclic heterocyclic moiety that is either saturated or partially unsaturated, and having, in addition to carbon atoms, one or more, preferably one to four, heteroatoms, as defined above. When used in reference to a ring atom of a heterocycle, the term “nitrogen” includes a substituted nitrogen. As an example, in a saturated or partially unsaturated ring having 0-3 heteroatoms selected from oxygen, sulfur or nitrogen, the nitrogen may be N (as in 3,4-dihydro-2H-pyrrolyl), NH (as in pyrrolidinyl), or ⁺NR (as in N-substituted pyrrolidinyl).

A heterocyclic ring can be attached to its pendant group at any heteroatom or carbon atom that results in a stable structure and any of the ring atoms can be optionally substituted. Examples of such saturated or partially unsaturated heterocyclic radicals include, without limitation, tetrahydrofuranyl, tetrahydrothiophenyl pyrrolidinyl, piperidinyl, pyrrolinyl, tetrahydroquinolinyl, tetrahydroisoquinolinyl, decahydroquinolinyl, oxazolidinyl, piperazinyl, dioxanyl, dioxolanyl, diazepinyl, oxazepinyl, thiazepinyl, morpholinyl, and quinuclidinyl. The terms “heterocycle,” “heterocyclyl,” “heterocyclyl ring,” “heterocyclic group,” “heterocyclic moiety,” and “heterocyclic radical,” are used interchangeably herein, and also include groups in which a heterocyclyl ring is fused to one or more aryl, heteroaryl, or cycloaliphatic rings, such as indolinyl, 3H-indolyl, chromanyl, phenanthridinyl, or tetrahydroquinolinyl, where the radical or point of attachment is on the heterocyclyl ring. A heterocyclyl group may be mono- or bicyclic. The term “heterocyclylalkyl” refers to an alkyl group substituted by a heterocyclyl, wherein the alkyl and heterocyclyl portions independently are optionally substituted.

As used herein, the term “partially unsaturated” refers to a ring moiety that includes at least one double or triple bond. The term “partially unsaturated” is intended to encompass rings having multiple sites of unsaturation, but is not intended to include aryl or heteroaryl moieties, as herein defined.

As described herein, compounds of the invention may contain “optionally substituted” moieties. In general, the term “substituted,” whether preceded by the term “optionally” or not, means that one or more hydrogens of the designated moiety are replaced with a suitable substituent. Unless otherwise indicated, an “optionally substituted” group may have a suitable substituent at each substitutable position of the group, and when more than one position in any given structure may be substituted with more than one substituent selected from a specified group, the substituent may be either the same or different at every position. Combinations of substituents envisioned by this invention are preferably those that result in the formation of stable or chemically feasible compounds. The term “stable,” as used herein, refers to compounds that are not substantially altered when subjected to conditions to allow for their production, detection, and, in certain embodiments, their recovery, purification, and use for one or more of the purposes disclosed herein.

Suitable monovalent substituents on a substitutable carbon atom of an “optionally substituted” group are independently halogen; —(CH₂)₀₋₄R^(o); —(CH₂)₀₋₄OR^(o); —O(CH₂)₀₋₄R^(o), —O—(CH₂)₀₋₄C(O)OR^(o); —(CH₂)₀₋₄CH(OR^(o))₂; —(CH₂)₀₋₄SR^(o); —(CH₂)₀₋₄Ph, which may be substituted with R^(o); —(CH₂)₀₋₄O(CH₂)₀₋₁Ph which may be substituted with R^(o); —CH═CHPh, which may be substituted with R^(o); —(CH₂)₀₋₄O(CH₂)₀₋₁-pyridyl which may be substituted with R^(o); —NO₂; —CN; —N₃; —(CH₂)₀₋₄N(R^(o))₂; —(CH₂)₀₋₄N(R^(o))C(O)R^(o); —N(R^(o))C(S)R^(o); —(CH₂)₀₋₄N(R^(o))C(O)NR^(o) ₂; —N(R^(o))C(S)NR^(o) ₂; —(CH₂)₀₋₄N(R^(o))C(O)OR^(o); —N(R^(o))N(R^(o))C(O)R^(o); —N(R^(o))N(R^(o))C(O)NR^(o) ₂; —N(R^(o))N(R^(o))C(O)OR^(o); —(CH₂)₀₋₄C(O)R^(o); —C(S)R^(o); —(CH₂)₀₋₄C(O)OR^(o); —(CH₂)₀₋₄C(O)SR^(o); —(CH₂)₀₋₄C(O)OSiR^(o) ₃; —(CH₂)₀₋₄OC(O)R^(o); —OC(O)(CH₂)₀₋₄SR—, SC(S)SR^(o); —(CH₂)₀₋₄SC(O)R^(o); —(CH₂)₀₋₄C(O)NR^(o) ₂; —C(S)NR^(o) ₂; —C(S)SR^(o); —SC(S)SR^(o), —(CH₂)₀₋₄OC(O)NR^(o) ₂; —C(O)N(OR^(o))R^(o); —C(O)C(O)R^(o); —C(O)CH₂C(O)R^(o); —C(NOR^(o))R^(o); —(CH₂)₀₋₄SSR^(o); —(CH₂)₀₋₄S(O)₂R^(o); —(CH₂)₀₋₄S(O)₂OR^(o); —(CH₂)₀₋₄OS(O)₂R^(o); —S(O)₂NR^(o) ₂; —(CH₂)₀₋₄S(O)R^(o); —N(R^(o))S(O)₂NR^(o) ₂; —N(R^(o))S(O)₂R^(o); —N(OR^(o))R^(o); —C(NH)NR^(o) ₂; —P(O)₂R^(o); —P(O)R^(o) ₂; —OP(O)R^(o) ₂; —OP(O)(OR^(o))₂; SiR^(o) ₃; —(C₁₋₄ straight or branched)alkylene)O—N(R^(o))₂; or —(C₁₋₄ straight or branched)alkylene)C(O)O—N(R^(o) ₂, wherein each R^(o) may be substituted as defined below and is independently hydrogen, C₁₋₆ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, —CH₂-(5-6 membered heteroaryl ring), or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R^(o), taken together with their intervening atom(s), form a 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, which may be substituted as defined below.

Suitable monovalent substituents on R^(o) (or the ring formed by taking two independent occurrences of R^(o) together with their intervening atoms), are independently halogen, —(CH₂)₀₋₂R^(●), -(haloR^(●)), —(CH₂)₀₋₂OH, —(CH₂)₀₋₂OR^(●), —(CH₂)₀₋₂CH(OR^(●))₂; —O(haloR^(●)), —CN, —N₃, —(CH₂)₀₋₂C(O)R^(●), —(CH₂)₀₋₂C(O)OH, —(CH₂)₀₋₂C(O)OR^(●), —(CH₂)₀₋₂SR^(●), —(CH₂)₀₋₂SH, —(CH₂)₀₋₂NH₂, —(CH₂)₀₋₂NHR^(●), —(CH₂)₀₋₂NR^(●) ₂, —NO₂, —SiR^(●) ₃, —OSiR^(●) ₃, —C(O)SR^(●), —(C₁₋₄ straight or branched alkylene)C(O)OR^(●), or —SSR^(●) wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently selected from C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents on a saturated carbon atom of R^(o) include ═O and ═S.

Suitable divalent substituents on a saturated carbon atom of an “optionally substituted” group include the following: ═O, ═S, ═NNR*₂, ═NNHC(O)R*, ═NNHC(O)OR*, ═NNHS(O)₂R*, ═NR*, ═NOR*, —O(C(R*₂))₂₋₃O—, or —S(C(R*₂))₂₋₃S—, wherein each independent occurrence of R* is selected from hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. Suitable divalent substituents that are bound to vicinal substitutable carbons of an “optionally substituted” group include: —O(CR*₂)₂₋₃O—, wherein each independent occurrence of R* is selected from hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on the aliphatic group of R* include halogen, —R^(●), -(haloR^(●)), —OH, —OR^(●), —O(haloR^(●)), —CN, —C(O)OH, —C(O)OR^(●), —NH₂, —NHR^(●), —NR^(●) ₂, or —NO₂, wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on a substitutable nitrogen of an “optionally substituted” group include —R^(\), —NR^(\) ₂, —C(O)R^(\), —C(O)OR^(\), —C(O)C(O)R^(\), —C(O)CH₂C(O)R^(\), —S(O)₂R^(\), —S(O)₂NR^(\) ₂, —C(S)NR^(\) ₂, —C(NH)NR^(\) ₂, or —N(R^(\))S(O)₂R^(\); wherein each R^(\) is independently hydrogen, C₁₋₆ aliphatic which may be substituted as defined below, unsubstituted —OPh, or an unsubstituted 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or, notwithstanding the definition above, two independent occurrences of R^(\), taken together with their intervening atom(s) form an unsubstituted 3-12-membered saturated, partially unsaturated, or aryl mono- or bicyclic ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

Suitable substituents on the aliphatic group of Rt are independently halogen, —R^(●), -(haloR^(●)), —OH, —OR^(●), —O(haloR^(●)), —CN, —C(O)OH, —C(O)OR^(●), —NH₂, —NHR^(●), —NR^(●) ₂, or —NO₂, wherein each R^(●) is unsubstituted or where preceded by “halo” is substituted only with one or more halogens, and is independently C₁₋₄ aliphatic, —CH₂Ph, —O(CH₂)₀₋₁Ph, or a 5-6-membered saturated, partially unsaturated, or aryl ring having 0-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.

As used herein, the term “pharmaceutically acceptable salt” refers to those salts which are, within the scope of sound medical judgment, suitable for use in contact with the tissues of humans and lower animals without undue toxicity, irritation, allergic response and the like, and are commensurate with a reasonable benefit/risk ratio. Pharmaceutically acceptable salts are well known in the art. For example, S. M. Berge et al., describe pharmaceutically acceptable salts in detail in J. Pharmaceutical Sciences, 1977, 66, 1-19, incorporated herein by reference. Pharmaceutically acceptable salts of the compounds of this invention include those derived from suitable inorganic and organic acids and bases. Examples of pharmaceutically acceptable, nontoxic acid addition salts are salts of an amino group formed with inorganic acids such as hydrochloric acid, hydrobromic acid, phosphoric acid, sulfuric acid and perchloric acid or with organic acids such as acetic acid, oxalic acid, maleic acid, tartaric acid, citric acid, succinic acid or malonic acid or by using other methods used in the art such as ion exchange. Other pharmaceutically acceptable salts include adipate, alginate, ascorbate, aspartate, benzenesulfonate, benzoate, bisulfate, borate, butyrate, camphorate, camphorsulfonate, citrate, cyclopentanepropionate, digluconate, dodecylsulfate, ethanesulfonate, formate, fumarate, glucoheptonate, glycerophosphate, gluconate, hemisulfate, heptanoate, hexanoate, hydroiodide, 2-hydroxy-ethanesulfonate, lactobionate, lactate, laurate, lauryl sulfate, malate, maleate, malonate, methanesulfonate, 2-naphthalenesulfonate, nicotinate, nitrate, oleate, oxalate, palmitate, pamoate, pectinate, persulfate, 3-phenylpropionate, phosphate, pivalate, propionate, stearate, succinate, sulfate, tartrate, thiocyanate, p-toluenesulfonate, undecanoate, valerate salts, and the like.

Salts derived from appropriate bases include alkali metal, alkaline earth metal, ammonium and N⁺(C₁₋₄alkyl)₄ salts. Representative alkali or alkaline earth metal salts include sodium, lithium, potassium, calcium, magnesium, and the like. Further pharmaceutically acceptable salts include, when appropriate, nontoxic ammonium, quaternary ammonium, and amine cations formed using counterions such as halide, hydroxide, carboxylate, sulfate, phosphate, nitrate, loweralkyl sulfonate and aryl sulfonate.

Unless otherwise stated, structures depicted herein are also meant to include all isomeric (e.g., enantiomeric, diastereomeric, and geometric (or conformational)) forms of the structure; for example, the R and S configurations for each asymmetric center, Z and E double bond isomers, and Z and E conformational isomers. Therefore, single stereochemical isomers as well as enantiomeric, diastereomeric, and geometric (or conformational) mixtures of the present compounds are within the scope of the invention. Unless otherwise stated, all tautomeric forms of the compounds of the invention are within the scope of the invention. Additionally, unless otherwise stated, structures depicted herein are also meant to include compounds that differ only in the presence of one or more isotopically enriched atoms. For example, compounds having the present structures including the replacement of hydrogen by deuterium or tritium, or the replacement of a carbon by a ¹³C- or ¹⁴C-enriched carbon are within the scope of this invention. Such compounds are useful, for example, as analytical tools, as probes in biological assays, or as therapeutic agents in accordance with the present invention. In certain embodiments, a warhead moiety, R³, of a provided compound comprises one or more deuterium atoms.

As used herein, the term “irreversible” or “irreversible inhibitor” refers to an inhibitor (i.e. a compound) that is able to be covalently bonded to HCV protease in a substantially non-reversible manner. That is, whereas a reversible inhibitor is able to bind to (but is generally unable to form a covalent bond with) HCV protease, and therefore can become dissociated from the HCV protease an irreversible inhibitor will remain substantially bound to HCV protease once covalent bond formation has occurred. Irreversible inhibitors usually display time dependency, whereby the degree of inhibition increases with the time with which the inhibitor is in contact with the enzyme. In certain embodiments, an irreversible inhibitor will remain substantially bound to HCV protease once covalent bond formation has occurred and will remain bound for a time period that is longer than the life of the protein.

Methods for identifying if a compound is acting as an irreversible inhibitor are known to one of ordinary skill in the art. Such methods include, but are not limited to, enzyme kinetic analysis of the inhibition profile of the compound with HCV protease, the use of mass spectrometry of the protein drug target modified in the presence of the inhibitor compound, discontinuous exposure, also known as “washout,” experiments, and the use of labeling, such as radiolabelled inhibitor, to show covalent modification of the enzyme, as well as other methods known to one of skill in the art.

One of ordinary skill in the art will recognize that certain reactive functional groups can act as “warheads.” As used herein, the term “warhead” or “warhead group” refers to a functional group present on a compound of the present invention wherein that functional group is capable of covalently binding to an amino acid residue (such as cysteine, lysine, histidine, or other residues capable of being covalently modified) present in the binding pocket of the target protein, thereby irreversibly inhibiting the protein. It will be appreciated that the -L-Y group, as defined and described herein, provides such warhead groups for covalently, and irreversibly, inhibiting the protein.

As used herein, the term “inhibitor” is defined as a compound that binds to and/or inhibits HCV protease with measurable affinity. In certain embodiments, an inhibitor has an IC₅₀ and/or binding constant of less about 50 μM, less than about 1 μM, less than about 500 nM, less than about 100 nM, less than about 10 nM, or less than about 1 nM.

A compound of the present invention may be tethered to a detectable moiety. One of ordinary skill in the art will recognize that a detectable moiety may be attached to a provided compound via a suitable substituent. As used herein, the term “suitable substituent” refers to a moiety that is capable of covalent attachment to a detectable moiety. Such moieties are well known to one of ordinary skill in the art and include groups containing, e.g., a carboxylate moiety, an amino moiety, a thiol moiety, or a hydroxyl moiety, to name but a few. It will be appreciated that such moieties may be directly attached to a provided compound or via a tethering group, such as a bivalent saturated or unsaturated hydrocarbon chain. In some embodiments, such moieties may be attached via click chemistry. In some embodiments, such moieties may be attached via a 1,3-cycloaddition of an azide with an alkyne, optionally in the presence of a copper catalyst. Methods of using click chemistry are known in the art and include those described by Rostovtsev et al., Angew. Chem. Int. Ed. 2002, 41, 2596-99 and Sun et al., Bioconjugate Chem., 2006, 17, 52-57.

As used herein, the term “detectable moiety” is used interchangeably with the term “label” and relates to any moiety capable of being detected, e.g., primary labels and secondary labels. Primary labels, such as radioisotopes (e.g., tritium, ³²P, ³³P, ³⁵S, or ¹⁴C), mass-tags, and fluorescent labels are signal generating reporter groups which can be detected without further modifications. Detectable moieties also include luminescent and phosphorescent groups.

The term “secondary label” as used herein refers to moieties such as biotin and various protein antigens that require the presence of a second intermediate for production of a detectable signal. For biotin, the secondary intermediate may include streptavidin-enzyme conjugates. For antigen labels, secondary intermediates may include antibody-enzyme conjugates. Some fluorescent groups act as secondary labels because they transfer energy to another group in the process of nonradiative fluorescent resonance energy transfer (FRET), and the second group produces the detected signal.

The terms “fluorescent label”, “fluorescent dye”, and “fluorophore” as used herein refer to moieties that absorb light energy at a defined excitation wavelength and emit light energy at a different wavelength. Examples of fluorescent labels include, but are not limited to: Alexa Fluor dyes (Alexa Fluor 350, Alexa Fluor 488, Alexa Fluor 532, Alexa Fluor 546, Alexa Fluor 568, Alexa Fluor 594, Alexa Fluor 633, Alexa Fluor 660 and Alexa Fluor 680), AMCA, AMCA-S, BODIPY dyes (BODIPY FL, BODIPY R6G, BODIPY TMR, BODIPY TR, BODIPY 530/550, BODIPY 558/568, BODIPY 564/570, BODIPY 576/589, BODIPY 581/591, BODIPY 630/650, BODIPY 650/665), Carboxyrhodamine 6G, carboxy-X-rhodamine (ROX), Cascade Blue, Cascade Yellow, Coumarin 343, Cyanine dyes (Cy3, Cy5, Cy3.5, Cy5.5), Dansyl, Dapoxyl, Dialkylaminocoumarin, 4′,5′-Dichloro-2′,7′-dimethoxy-fluorescein, DM-NERF, Eosin, Erythrosin, Fluorescein, FAM, Hydroxycoumarin, IRDyes (IRD40, IRD 700, IRD 800), JOE, Lissamine rhodamine B, Marina Blue, Methoxycoumarin, Naphthofluorescein, Oregon Green 488, Oregon Green 500, Oregon Green 514, Pacific Blue, PyMPO, Pyrene, Rhodamine B, Rhodamine 6G, Rhodamine Green, Rhodamine Red, Rhodol Green, 2′,4′,5′,7′-Tetra-bromosulfone-fluorescein, Tetramethyl-rhodamine (TMR), Carboxytetramethylrhodamine (TAMRA), Texas Red, Texas Red-X.

The term “mass-tag” as used herein refers to any moiety that is capable of being uniquely detected by virtue of its mass using mass spectrometry (MS) detection techniques. Examples of mass-tags include electrophore release tags such as N-[3-[4′-[(p-Methoxytetrafluorobenzyl)oxy]phenyl]-3-methylglyceronyl]isonipecotic Acid, 4′-[2,3,5,6-Tetrafluoro-4-(pentafluorophenoxyl)]methyl acetophenone, and their derivatives. The synthesis and utility of these mass-tags is described in U.S. Pat. Nos. 4,650,750, 4,709,016, 5,360,8191, 5,516,931, 5,602,273, 5,604,104, 5,610,020, and 5,650,270. Other examples of mass-tags include, but are not limited to, nucleotides, dideoxynucleotides, oligonucleotides of varying length and base composition, oligopeptides, oligosaccharides, and other synthetic polymers of varying length and monomer composition. A large variety of organic molecules, both neutral and charged (biomolecules or synthetic compounds) of an appropriate mass range (100-2000 Daltons) may also be used as mass-tags.

The terms “measurable affinity” and “measurably inhibit,” as used herein, means a measurable change in HCV protease activity between a sample comprising a compound of the present invention, or composition thereof, and HCV protease, and an equivalent sample comprising HCV protease, in the absence of said compound, or composition thereof.

3. Description of Exemplary Compounds

In certain embodiments, the present invention provides a compound of formula I:

or a pharmaceutically acceptable salt thereof, wherein:

-   one of R^(a) and R^(b) is hydrogen and the other is —OH or —OC(O)R′,     or R^(a) and R^(b) are taken together to form an oxo group; -   R′ is an optionally substituted group selected from C₁₋₆ aliphatic,     C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered heteroaryl having     1-4 heteroatoms independently selected from nitrogen, oxygen, or     sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R^(x) and R^(y) are taken together to form an optionally substituted     C₃₋₇ membered ring having 0-2 heteroatoms independently selected     from nitrogen, oxygen, or sulfur; -   R¹ is an optionally substituted group selected from C₁₋₆ aliphatic     or C₃₋₇ cycloalkyl(C₁₋₃ alkyl); -   R² is hydrogen or an optionally substituted group selected from C₁₋₆     aliphatic or C₃₋₇ cycloalkyl; -   R³ is —(CH₂)_(n)-L-Y, wherein:     -   n is an integer from 0 to 5, inclusive;     -   L is a covalent bond or a bivalent C₁₋₈ saturated or         unsaturated, straight or branched, hydrocarbon chain, wherein         one, two, or three methylene units of L are optionally and         independently replaced by cyclopropylene, —NR—, —N(R)C(O)—,         —C(O)N(R)—, —N(R)SO₂—, —SO₂N(R)—, —O—, —C(O)—, —OC(O)—, —C(O)O—,         —S—, —SO—, —SO₂—, —C(═S)—, —C(═NR)—, —N═N—, or —C(═N₂)—;     -   Y is hydrogen, C₁₋₆ aliphatic optionally substituted with oxo,         halogen, NO₂, or CN, or a 3-10 membered monocyclic or bicyclic,         saturated, partially unsaturated, or aryl ring having 0-3         heteroatoms independently selected from nitrogen, oxygen, or         sulfur, and wherein said ring is substituted with 1-4 R^(e)         groups; and     -   each R^(e) is independently selected from -Q-Z, oxo, NO₂,         halogen, CN, a suitable leaving group, or C₁₋₆ aliphatic         optionally substituted with oxo, halogen, NO₂, or CN, wherein:         -   Q is a covalent bond or a bivalent C₁₋₆ saturated or             unsaturated, straight or branched, hydrocarbon chain,             wherein one or two methylene units of Q are optionally and             independently replaced by —N(R)—, —S—, —O—, —C(O)—, —OC(O)—,             —C(O)O—, —SO—, or —SO₂—, —N(R)C(O)—, —C(O)N(R)—, —N(R)SO₂—,             or —SO₂N(R)—; and         -   Z is hydrogen or C₁₋₆ aliphatic optionally substituted with             oxo, halogen, NO₂, or CN; -   R⁴ is —NHC(O)NHR⁵, —NHC(O)OR⁶, or

-   R⁵ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R⁶ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; -   R⁷ is an optionally substituted group selected from C₁₋₆ aliphatic,     bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl     having 1-4 heteroatoms independently selected from nitrogen, oxygen,     or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms     independently selected from nitrogen, oxygen, or sulfur; and -   R is hydrogen or an optionally substituted group selected from C₁₋₆     aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered     heteroaryl having 1-4 heteroatoms independently selected from     nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2     heteroatoms independently selected from nitrogen, oxygen, or sulfur.

In certain embodiments, n is an integer from 1 to 5, inclusive. In certain embodiments, n is 0. In certain embodiments, n is 1. In certain embodiments, n is 2. In certain embodiments, n is 3. In certain embodiments, n is 4. In certain embodiments, n is 5.

In certain embodiments, L is a covalent bond.

In certain embodiments, L is a bivalent C₁₋₈ saturated or unsaturated, straight or branched, hydrocarbon chain. In certain embodiments, L is —CH₂—.

In certain embodiments, L is a covalent bond, —CH₂—, —NH—, —CH₂NH—, —NHCH₂—, —NHC(O)—, —NHC(O)CH₂OC(O)—, —CH₂NHC(O)—, —NHSO₂—, —NHSO₂CH₂—, —NHC(O)CH₂OC(O)—, or —SO₂NH—.

In some embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two additional methylene units of L are optionally and independently replaced by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, —C(O)O—, cyclopropylene, —O—, —N(R)—, or —C(O)—.

In certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—.

In some embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—.

As described above, in certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond. One of ordinary skill in the art will recognize that such a double bond may exist within the hydrocarbon chain backbone or may be “exo” to the backbone chain and thus forming an alkylidene group. By way of example, such an L group having an alkylidene branched chain includes —CH₂C(═CH₂)CH₂—. Thus, in some embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond. Exemplary L groups include —NHC(O)C(═CH₂)CH₂—.

In certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—. In certain embodiments, L is —C(O)CH═CH(CH₃)—, —C(O)CH═CHCH₂NH(CH₃)—, —C(O)CH═CH(CH₃)—, —C(O)CH═CH—, —CH₂C(O)CH═CH—, —CH₂C(O)CH═CH(CH₃)—, —CH₂CH₂C(O)CH═CH—, —CH₂CH₂C(O)CH═CHCH₂—, —CH₂CH₂C(O)CH═CHCH₂NH(CH₃)—, or —CH₂CH₂C(O)CH═CH(CH₃)—, or —CH(CH₃)OC(O)CH═CH—.

In certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —OC(O)—.

In some embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—, and one or two additional methylene units of L are optionally and independently replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—. In some embodiments, L is —CH₂OC(O)CH═CHCH₂—, —CH₂—OC(O)CH═CH—, or —CH(CH═CH₂)OC(O)CH═CH—.

In certain embodiments, L is —NRC(O)CH═CH—, —NRC(O)CH═CHCH₂N(CH₃)—, —NRC(O)CH═CHCH₂O—, —CH₂NRC(O)CH═CH—, —NRSO₂CH═CH—, —NRSO₂CH═CHCH₂—, —NRC(O)(C═N₂)C(O)—, —NRC(O)CH═CHCH₂N(CH₃)—, —NRSO₂CH═CH—, —NRSO₂CH═CHCH₂—, —NRC(O)CH═CHCH₂O—, —NRC(O)C(═CH₂)CH₂—, —CH₂NRC(O)—, —CH₂NRC(O)CH═CH—, —CH₂CH₂NRC(O)—, or —CH₂NRC(O)cyclopropylene-, wherein each R is independently hydrogen or optionally substituted C₁₋₆ aliphatic.

In certain embodiments, L is —NHC(O)CH═CH—, —NHC(O)CH═CHCH₂N(CH₃)—, —NHC(O)CH═CHCH₂O—, —CH₂NHC(O)CH═CH—, —NHSO₂CH═CH—, —NHSO₂CH═CHCH₂—, —NHC(O)(C═N₂)C(O)—, —NHC(O)CH═CHCH₂N(CH₃)—, —NHSO₂CH═CH—, —NHSO₂CH═CHCH₂—, —NHC(O)CH═CHCH₂O—, —NHC(O)C(═CH₂)CH₂—, —CH₂NHC(O)—, —CH₂NHC(O)CH═CH—, —CH₂CH₂NHC(O)—, or —CH₂NHC(O)cyclopropylene-.

In some embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one triple bond. In certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one triple bond and one or two additional methylene units of L are optionally and independently replaced by —NRC(O)—, —C(O)NR—, —S—, —S(O)—, —SO₂—, —C(═S)—, —C(═NR)—, —O—, —N(R)—, or —C(O)—. In some embodiments, L has at least one triple bond and at least one methylene unit of L is replaced by —N(R)—, —N(R)C(O)—, —C(O)—, —C(O)O—, or —OC(O)—, or —O—.

Exemplary L groups include —C≡C—, —C≡CCH₂N(isopropyl)-, —NHC(O)C≡CCH₂CH₂—, —CH₂—C≡C—CH₂—, —C≡CCH₂O—, —CH₂C(O)C≡C—, —C(O)C≡C—, or —CH₂OC(═O)C≡C—.

In certain embodiments, L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein one methylene unit of L is replaced by cyclopropylene and one or two additional methylene units of L are independently replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO₂—, or —SO₂N(R)—. Exemplary L groups include —NHC(O)-cyclopropylene-SO₂— and —NHC(O)— cyclopropylene-.

As defined generally above, Y is hydrogen, C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN, or a 3-10 membered monocyclic or bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein said ring is substituted with at 1-4 R^(e) groups, each R^(e) is independently selected from -Q-Z, oxo, NO₂, halogen, CN, or C₁₋₆ aliphatic, wherein Q is a covalent bond or a bivalent C₁₋₆ saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by —N(R)—, —S—, —O—, —C(O)—, —OC(O)—, —C(O)O—, —SO—, or —SO₂—, —N(R)C(O)—, —C(O)N(R)—, —N(R)SO₂—, or —SO₂N(R)—; and, Z is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN.

In certain embodiments, Y is hydrogen.

In certain embodiments, Y is C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN. In some embodiments, Y is C₂₋₆ alkenyl optionally substituted with oxo, halogen, NO₂, or CN. In other embodiments, Y is C₂₋₆ alkynyl optionally substituted with oxo, halogen, NO₂, or CN. In some embodiments, Y is C₂₋₆ alkenyl. In other embodiments, Y is C₂₋₄ alkynyl.

In other embodiments, Y is C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN. Such Y groups include —CH₂F, —CH₂CN, —CH₂CN, and —CH₂NO₂.

In certain embodiments, Y is a saturated 3-6 membered monocyclic ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein Y is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein.

In some embodiments, Y is a saturated 3-4 membered heterocyclic ring having 1 heteroatom selected from oxygen or nitrogen wherein said ring is substituted with 1-2 R^(e) groups, wherein each R^(e) is as defined above and described herein. Exemplary such rings are epoxide and oxetane rings, wherein each ring is substituted with 1-2 R^(e) groups, wherein each R^(e) is as defined above and described herein.

In other embodiments, Y is a saturated 5-6 membered heterocyclic ring having 1-2 heteroatom selected from oxygen or nitrogen wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. Such rings include piperidine and pyrrolidine, wherein each ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In certain embodiments, Y is

wherein each R, Q, Z, and R^(e) is as defined above and described herein.

In some embodiments, Y is a saturated 3-6 membered carbocyclic ring, wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In certain embodiments, Y is cyclopropyl, cyclobutyl, cyclopentyl, or cyclohexyl, wherein each ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In certain embodiments, Y is

wherein R^(e) is as defined above and described herein. In certain embodiments, Y is cyclopropyl optionally substituted with halogen, CN or NO₂.

In certain embodiments, Y is a partially unsaturated 3-6 membered monocyclic ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein.

In some embodiments, Y is a partially unsaturated 3-6 membered carbocyclic ring, wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In some embodiments, Y is cyclopropenyl, cyclobutenyl, cyclopentenyl, or cyclohexenyl wherein each ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In certain embodiments, Y is

wherein each R^(e) is as defined above and described herein.

In certain embodiments, Y is a partially unsaturated 4-6 membered heterocyclic ring having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein. In certain embodiments, Y is selected from:

wherein each R and R^(e) is as defined above and described herein.

In certain embodiments, Y is a 6-membered aromatic ring having 0-2 nitrogens wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) group is as defined above and described herein. In certain embodiments, Y is phenyl, pyridyl, or pyrimidinyl, wherein each ring is substituted with 1-4 R^(e) groups, wherein each R^(e) is as defined above and described herein.

In some embodiments, Y is selected from:

wherein each R^(e) is as defined above and described herein.

In other embodiments, Y is a 5-membered heteroaryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-3 R^(e) groups, wherein each R^(e) group is as defined above and described herein. In some embodiments, Y is a 5 membered partially unsaturated or aryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, and sulfur, wherein said ring is substituted with 1-4 R^(e) groups, wherein each R^(e) group is as defined above and described herein. Exemplary such rings are isoxazolyl, oxazolyl, thiazolyl, imidazolyl, pyrazolyl, pyrrolyl, furanyl, thienyl, triazole, thiadiazole, and oxadiazole, wherein each ring is substituted with 1-3 R^(e) groups, wherein each R^(e) group is as defined above and described herein. In certain embodiments, Y is selected from:

wherein each R and R^(e) is as defined above and described herein.

In certain embodiments, Y is an 8-10 membered bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R^(e) groups, wherein R^(e) is as defined above and described herein. According to another aspect, Y is a 9-10 membered bicyclic, partially unsaturated, or aryl ring having 1-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, wherein said ring is substituted with 1-4 R^(e) groups, wherein R^(e) is as defined above and described herein. Exemplary such bicyclic rings include 2,3-dihydrobenzo[d]isothiazole, wherein said ring is substituted with 1-4 R^(e) groups, wherein R^(e) is as defined above and described herein.

As defined generally above, each R^(e) group is independently selected from -Q-Z, oxo, NO₂, halogen, CN, a suitable leaving group, or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN, wherein Q is a covalent bond or a bivalent C₁₋₆ saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by —N(R)—, —S—, —O—, —C(O)—, —OC(O)—, —C(O)O—, —SO—, or —SO₂—, —N(R)C(O)—, —C(O)N(R)—, —N(R)SO₂—, or —SO₂N(R)—; and Z is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN.

In certain embodiments, R^(e) is C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN. In other embodiments, R^(e) is oxo, NO₂, halogen, or CN.

In some embodiments, R^(e) is -Q-Z, wherein Q is a covalent bond and Z is hydrogen (i.e., R^(e) is hydrogen). In other embodiments, R^(e) is -Q-Z, wherein Q is a bivalent C₁₋₆ saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by —NR—, —NRC(O)—, —C(O)NR—, —S—, —O—, —C(O)—, —SO—, or —SO₂—. In other embodiments, Q is a bivalent C₂₋₆ straight or branched, hydrocarbon chain having at least one double bond, wherein one or two methylene units of Q are optionally and independently replaced by —NR—, —NRC(O)—, —C(O)NR—, —S—, —O—, —C(O)—, —SO—, or —SO₂—. In certain embodiments, the Z moiety of the R^(e) group is hydrogen. In some embodiments, -Q-Z is —NHC(O)CH═CH₂ or —C(O)CH═CH₂.

In certain embodiments, each R^(e) is independently selected from oxo, NO₂, CN, fluoro, chloro, —NHC(O)CH═CH₂, —C(O)CH═CH₂, —CH₂CH═CH₂, —C≡CH, —C(O)OCH₂Cl, —C(O)OCH₂F, —C(O)OCH₂CN, —C(O)CH₂Cl, —C(O)CH₂F, —C(O)CH₂CN, or —CH₂C(O)CH₃.

In certain embodiments, R^(e) is a suitable leaving group, ie a group that is subject to nucleophilic displacement. A “suitable leaving” is a chemical group that is readily displaced by a desired incoming chemical moiety such as the thiol moiety of a cysteine of interest. Suitable leaving groups are well known in the art, e.g., see, “Advanced Organic Chemistry,” Jerry March, 5^(th) Ed., pp. 351-357, John Wiley and Sons, N.Y. Such leaving groups include, but are not limited to, halogen, alkoxy, sulphonyloxy, optionally substituted alkylsulphonyloxy, optionally substituted alkenylsulfonyloxy, optionally substituted arylsulfonyloxy, acyl, and diazonium moieties. Examples of suitable leaving groups include chloro, iodo, bromo, fluoro, acetyl, methanesulfonyloxy (mesyloxy), tosyloxy, triflyloxy, nitro-phenylsulfonyloxy (nosyloxy), and bromo-phenylsulfonyloxy (brosyloxy).

In certain embodiments, the following embodiments and combinations of -L-Y apply:

-   -   (a) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one double bond and one or two additional         methylene units of L are optionally and independently replaced         by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—,         —OC(O)—, —C(O)O—, cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y         is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo,         halogen, NO₂, or CN; or     -   (b) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one double bond and at least one         methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—,         —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—,         and one or two additional methylene units of L are optionally         and independently replaced by cyclopropylene, —O—, —N(R)—, or         —C(O)—; and Y is hydrogen or C₁₋₆ aliphatic optionally         substituted with oxo, halogen, NO₂, or CN; or     -   (c) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one double bond and at least one         methylene unit of L is replaced by —C(O)—, and one or two         additional methylene units of L are optionally and independently         replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y is         hydrogen or C₁₋₆ aliphatic optionally substituted with oxo,         halogen, NO₂, or CN; or     -   (d) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one double bond and at least one         methylene unit of L is replaced by —C(O)—; and Y is hydrogen or         C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or         CN; or     -   (e) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one double bond and at least one         methylene unit of L is replaced by —OC(O)—; and Y is hydrogen or         C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or         CN; or     -   (f) L is —NRC(O)CH═CH—, —NRC(O)CH═CHCH₂N(CH₃)—,         —NRC(O)CH═CHCH₂O—, —CH₂NRC(O)CH═CH—, —NRSO₂CH═CH—,         —NRSO₂CH═CHCH₂—, —NRC(O)(C═N₂)—, —NRC(O)(C═N₂)C(O)—,         —NRC(O)CH═CHCH₂N(CH₃)—, —NRSO₂CH═CH—, —NRSO₂CH═CHCH₂—,         —NRC(O)CH═CHCH₂O—, —NRC(O)C(═CH₂)CH₂—, —CH₂NRC(O)—,         —CH₂NRC(O)CH═CH—, —CH₂CH₂NRC(O)—, or —CH₂NRC(O)cyclopropylene-;         wherein R is H or optionally substituted C₁₋₆ aliphatic; and Y         is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo,         halogen, NO₂, or CN; or     -   (g) L is —NHC(O)CH═CH—, —NHC(O)CH═CHCH₂N(CH₃)—,         —NHC(O)CH═CHCH₂O—, —CH₂NHC(O)CH═CH—, —NHSO₂CH═CH—,         —NHSO₂CH═CHCH₂—, —NHC(O)(C═N₂)—, —NHC(O)(C═N₂)C(O)—,         —NHC(O)CH═CHCH₂N(CH₃)—, —NHSO₂CH═CH—, —NHSO₂CH═CHCH₂—,         —NHC(O)CH═CHCH₂O—, —NHC(O)C(═CH₂)CH₂—, —CH₂NHC(O)—,         —CH₂NHC(O)CH═CH—, —CH₂CH₂NHC(O)—, or —CH₂NHC(O)cyclopropylene-;         and Y is hydrogen or C₁₋₆ aliphatic optionally substituted with         oxo, halogen, NO₂, or CN; or     -   (h) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one alkylidenyl double bond and at least         one methylene unit of L is replaced by —C(O)—, —NRC(O)—,         —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or         —C(O)O—, and one or two additional methylene units of L are         optionally and independently replaced by cyclopropylene, —O—,         —N(R)—, or —C(O)—; and Y is hydrogen or C₁₋₆ aliphatic         optionally substituted with oxo, halogen, NO₂, or CN; or     -   (i) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein L has at least one triple bond and one or two additional         methylene units of L are optionally and independently replaced         by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—,         —OC(O)—, or —C(O)O—, and Y is hydrogen or C₁₋₆ aliphatic         optionally substituted with oxo, halogen, NO₂, or CN; or     -   (j) L is —C≡C—, —C≡CCH₂N(isopropyl)-, —NHC(O)C≡CCH₂CH₂—,         —CH₂—C≡C—CH₂—, —C≡CCH₂O—, —CH₂C(O)C≡C—, —C(O)C≡C—, or         —CH₂OC(═O)C≡C—; and Y is hydrogen or C₁₋₆ aliphatic optionally         substituted with oxo, halogen, NO₂, or CN; or     -   (k) L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain         wherein one methylene unit of L is replaced by cyclopropylene         and one or two additional methylene units of L are independently         replaced by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—,         —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—; and Y is hydrogen or C₁₋₆         aliphatic optionally substituted with oxo, halogen, NO₂, or CN;         or     -   (l) L is a covalent bond and Y is selected from:         -   (i) C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN;         -   (ii) C₂₋₆ alkenyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iii) C₂₋₆ alkynyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iv) a saturated 3-4 membered heterocyclic ring having 1             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-2 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (v) a saturated 5-6 membered heterocyclic ring having 1-2             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (vi)

-   -   -    wherein each R, Q, Z, and R^(e) is as defined above and             described herein; or         -   (vii) a saturated 3-6 membered carbocyclic ring, wherein             said ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (viii) a partially unsaturated 3-6 membered monocyclic ring             having 0-3 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (ix) a partially unsaturated 3-6 membered carbocyclic ring,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) is as defined above and described herein;             or         -   (x)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xi) a partially unsaturated 4-6 membered heterocyclic ring             having 1-2 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (xii)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xiii) a 6-membered aromatic ring having 0-2 nitrogens             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xiv)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xv) a 5-membered heteroaryl ring having 1-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-3 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xvi)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xvii) an 8-10 membered bicyclic, saturated, partially             unsaturated, or aryl ring having 0-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein R^(e) is as defined above and described herein;

    -   (m) L is —C(O)— and Y is selected from:         -   (i) C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN; or         -   (ii) C₂₋₆ alkenyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iii) C₂₋₆ alkynyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iv) a saturated 3-4 membered heterocyclic ring having 1             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-2 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (v) a saturated 5-6 membered heterocyclic ring having 1-2             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (vi)

-   -   -    wherein each R, Q, Z, and R^(e) is as defined above and             described herein; or         -   (vii) a saturated 3-6 membered carbocyclic ring, wherein             said ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (viii) a partially unsaturated 3-6 membered monocyclic ring             having 0-3 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (ix) a partially unsaturated 3-6 membered carbocyclic ring,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) is as defined above and described herein;         -   (x)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xi) a partially unsaturated 4-6 membered heterocyclic ring             having 1-2 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (xii)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xiii) a 6-membered aromatic ring having 0-2 nitrogens             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xiv)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xv) a 5-membered heteroaryl ring having 1-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-3 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xvi)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xvii) an 8-10 membered bicyclic, saturated, partially             unsaturated, or aryl ring having 0-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein R^(e) is as defined above and described herein;

    -   (n) L is —N(R)C(O)— and Y is selected from:         -   (i) C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN; or         -   (ii) C₂₋₆ alkenyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iii) C₂₋₆ alkynyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iv) a saturated 3-4 membered heterocyclic ring having 1             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-2 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (v) a saturated 5-6 membered heterocyclic ring having 1-2             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (vi)

-   -   -    wherein each R, Q, Z, and R^(e) is as defined above and             described herein; or         -   (vii) a saturated 3-6 membered carbocyclic ring, wherein             said ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (viii) a partially unsaturated 3-6 membered monocyclic ring             having 0-3 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (ix) a partially unsaturated 3-6 membered carbocyclic ring,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) is as defined above and described herein;         -   (x)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xi) a partially unsaturated 4-6 membered heterocyclic ring             having 1-2 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (xii)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xiii) a 6-membered aromatic ring having 0-2 nitrogens             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xiv)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xv) a 5-membered heteroaryl ring having 1-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-3 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xvi)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xvii) an 8-10 membered bicyclic, saturated, partially             unsaturated, or aryl ring having 0-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein R^(e) is as defined above and described herein;

    -   (o) L is a bivalent C₁₋₈ saturated or unsaturated, straight or         branched, hydrocarbon chain; and Y is selected from:         -   (i) C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN;         -   (ii) C₂₋₆ alkenyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iii) C₂₋₆ alkynyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iv) a saturated 3-4 membered heterocyclic ring having 1             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-2 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (v) a saturated 5-6 membered heterocyclic ring having 1-2             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (vi)

-   -   -    wherein each R, Q, Z, and R^(e) is as defined above and             described herein; or         -   (vii) a saturated 3-6 membered carbocyclic ring, wherein             said ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (viii) a partially unsaturated 3-6 membered monocyclic ring             having 0-3 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (ix) a partially unsaturated 3-6 membered carbocyclic ring,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) is as defined above and described herein;         -   (x)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xi) a partially unsaturated 4-6 membered heterocyclic ring             having 1-2 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (xii)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xiii) a 6-membered aromatic ring having 0-2 nitrogens             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xiv)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xv) a 5-membered heteroaryl ring having 1-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-3 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xvi)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xvii) an 8-10 membered bicyclic, saturated, partially             unsaturated, or aryl ring having 0-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein R^(e) is as defined above and described herein;

    -   (p) L is a covalent bond, —CH₂—, —NH—, —C(O)—, —CH₂NH—, —NHCH₂—,         —NHC(O)—, —NHC(O)CH₂OC(O)—, —CH₂NHC(O)—, —NHSO₂—, —NHSO₂CH₂—,         —NHC(O)CH₂OC(O)—, or —SO₂NH—; and Y is selected from:         -   (i) C₁₋₆ alkyl substituted with oxo, halogen, NO₂, or CN; or         -   (ii) C₂₋₆ alkenyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iii) C₂₋₆ alkynyl optionally substituted with oxo, halogen,             NO₂, or CN; or         -   (iv) a saturated 3-4 membered heterocyclic ring having 1             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-2 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (v) a saturated 5-6 membered heterocyclic ring having 1-2             heteroatom selected from oxygen or nitrogen wherein said             ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (vi)

-   -   -    wherein each R, Q, Z, and R^(e) is as defined above and             described herein; or         -   (vii) a saturated 3-6 membered carbocyclic ring, wherein             said ring is substituted with 1-4 R^(e) groups, wherein each             R^(e) is as defined above and described herein; or         -   (viii) a partially unsaturated 3-6 membered monocyclic ring             having 0-3 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (ix) a partially unsaturated 3-6 membered carbocyclic ring,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) is as defined above and described herein;         -   (x)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xi) a partially unsaturated 4-6 membered heterocyclic ring             having 1-2 heteroatoms independently selected from nitrogen,             oxygen, or sulfur, wherein said ring is substituted with 1-4             R^(e) groups, wherein each R^(e) is as defined above and             described herein; or         -   (xii)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xiii) a 6-membered aromatic ring having 0-2 nitrogens             wherein said ring is substituted with 1-4 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xiv)

-   -   -    wherein each R^(e) is as defined above and described             herein; or         -   (xv) a 5-membered heteroaryl ring having 1-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-3 R^(e) groups,             wherein each R^(e) group is as defined above and described             herein; or         -   (xvi)

-   -   -    wherein each R and R^(e) is as defined above and described             herein; or         -   (xvii) an 8-10 membered bicyclic, saturated, partially             unsaturated, or aryl ring having 0-3 heteroatoms             independently selected from nitrogen, oxygen, or sulfur,             wherein said ring is substituted with 1-4 R^(e) groups,             wherein R^(e) is as defined above and described herein.

In certain embodiments, the Y group of formula I is selected from those set forth in Table 1, below, wherein each wavy line indicates the point of attachment to the rest of the molecule.

TABLE 1 Exemplary Y groups:

a

b

c

d

e

f

g

h

i

j

k

l

m

n

o

p

q

r

s

t

u

v

w

x

y

z

aa

bb

cc

dd

ee

ff

gg

hh

ii

jj

kk

ll

mm

nn

oo

pp

qq

rr

ss

tt

uu

vv

ww

xx

yy

zz

aaa

bbb

ccc

ddd

eee

fff

ggg

hhh

iii

jjj

kkk

lll

mmm

nnn

ooo

ppp

qqq

rrr

sss

ttt

uuu

vvv

qqq

www

xxx

yyy

zzz

aaaa

bbbb

cccc

dddd

eeee

ffff

gggg

hhhh

iiii

jjjj

kkkk

llll

mmmm

nnnn

oooo

pppp

qqqq

rrrr

ssss

tttt

uuuu

vvvv

wwww

xxxx

yyyy

zzzz

aaaaa

bbbbb

ccccc wherein each R^(e) group depicted in Table 1 is independently selected from halogen.

In certain embodiments, R³ is —C≡CH, —C≡CCH₂NH(isopropyl), —NHC(O)C≡CCH₂CH₃, —CH₂—C≡C—CH₃, —C≡CCH₂OH, —CH₂C(O)C≡CH, —C(O)C≡CH, or —CH₂OC(═O)C≡CH. In some embodiments, R³ is selected from —NHC(O)CH═CH₂, —NHC(O)CH═CHCH₂N(CH₃)₂, or —CH₂NHC(O)CH═CH₂.

In certain embodiments, R³ is selected from those set forth in Table 2, below, wherein each wavy line indicates the point of attachment to the rest of the molecule.

TABLE 2 Exemplary R³ Groups

a

b

c

d

e

f

g

h

i

j

k

l

m

n

o

p

q

r

s

t

u

v

w

x

y

z

aa

bb

cc

dd

ee

ff

gg

hh

ii

jj

kk

ll

mm

nn

oo

pp

qq

rr

ss

tt

uu

vv

ww

xx

yy

zz

aaa

bbb

ccc

ddd

eee

fff

ggg

hhh

iii

jjj

kkk

lll

mmm

nnn

ooo

ppp

qqq

rrr

sss

ttt

uuu

vvv

www

xxx

yyy

zzz

aaaa

bbbb

cccc

dddd

eeee

ffff

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xxxxxx wherein each R^(e) is independently a suitable leaving group, NO₂, CN, or oxo.

In certain embodiments, one of R^(a) and R^(b) is hydrogen and the other is —OH or —OC(O)R′. In other embodiments, R^(a) and R^(b) are taken together to form an oxo group. In certain embodiments, one of R^(a) and R^(b) is hydrogen and the other is —OH. In certain embodiments, one of R^(a) and R^(b) is hydrogen and the other is —OC(O)R′. In some embodiments, wherein one of R^(a) and R^(b) is —OC(O)R′, R′ is an optionally substituted group selected from C₁₋₆ aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, or 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R′ is substituted C₁₋₆ aliphatic. In some embodiments, R′ is trifluoromethyl.

In certain embodiments, R¹ is an optionally substituted C₁₋₆ aliphatic group. In some embodiments, R¹ is optionally substituted C₁₋₃ aliphatic. In some embodiments, R¹ is n-propyl. In some embodiments, R¹ is an optionally substituted C₃₋₇ cycloalkyl(C₁₋₃ alkyl) group. In some embodiments, R¹ is an optionally substituted C₄₋₆ cycloalkyl(C₁₋₃ alkyl) group. In some embodiments, R¹ is

In certain embodiments, R² is hydrogen. In certain embodiments, R² is an optionally substituted group selected from C₁₋₆ aliphatic or C₃₋₇ cycloalkyl. In some embodiments, R² is C₃₋₇ cycloalkyl. In some embodiments, R² is cyclopropyl.

As described above, the R^(x) and R^(y) groups of formula I are taken together to form an optionally substituted C₃₋₇ membered ring having 0-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, the R^(x) and R^(y) groups of formula I are taken together to form an optionally substituted C₃₋₇ membered carbocyclic ring. In some embodiments, the R^(x) and R^(y) groups of formula I are taken together to form an optionally substituted cyclopropyl ring. In some embodiments, the R^(x) and R^(y) groups of formula I are taken together to form an optionally substituted cyclopentyl ring.

In certain embodiments, the R⁴ group of formula I is —NHC(O)NHR⁵. In some embodiments, the R⁴ group of formula I is —NHC(O)OR⁶. In other embodiments, the R⁴ group of formula I is

As described above, the R⁵, R⁶, and R⁷ groups of formula I are independently optionally substituted groups selected from optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R⁵ is an optionally substituted 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and R⁷ is an optionally substituted C₁₋₆ aliphatic group. In some embodiments, R⁵ is

and R⁷ is cyclohexyl.

In certain embodiments, R⁴ is —NHC(O)NHR⁵, wherein R⁵ is an optionally substituted group selected from optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R⁵ is optionally substituted C₁₋₆ aliphatic. In some embodiments, R⁵ is t-butyl.

In certain embodiments, R⁴ is —NHC(O)OR⁶, wherein R⁶ is an optionally substituted group selected from optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R⁶ is optionally substituted C₁₋₆ aliphatic. In some embodiments, R⁶ is t-butyl.

In certain embodiments, the R⁵ group of formula I is an optionally substituted 5-10 membered heteroaryl ring having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R⁵ is an optionally substituted 6-membered heteroaryl ring having 1-2 nitrogens. In certain embodiments, R⁵ is

In certain embodiments, the R⁷ group of formula I is an optionally substituted C₁₋₆ aliphatic group. In some embodiments, R⁷ is a branched C₁₋₅ alkyl group. In some embodiments, R⁷ is an optionally substituted C₃₋₇ cycloalkyl group. In some embodiments, R⁷ is cyclohexyl.

In certain embodiments, R^(x) and R^(y) are taken together to form a cyclopentyl ring. Thus, the present invention provides a compound of formula II-a:

or a pharmaceutically acceptable salt thereof, wherein each of R¹, R², R³, R⁵, R⁷, R^(a), and R^(b) is as defined above for formula I and described in classes and subclasses above and herein.

In some embodiments, the R¹ group of formula II-a is optionally substituted C₁₋₆ aliphatic. In some embodiments, R¹ is n-propyl.

In certain embodiments, the R² group of formula II-a is an optionally substituted C₃₋₇ cycloalkyl group. In certain embodiments, R² is cyclopropyl. In some embodiments, R² is hydrogen.

In some embodiments, the R⁵ group of formula II-a is an optionally substituted 5-10 membered heteroaryl group having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R⁵ is

In some embodiments, the R⁷ group of formula II-a is an optionally substituted C₃₋₇ cycloalkyl group. In some embodiments, R⁷ is cyclohexyl.

Exemplary R³ groups of formula II-a include those described above and herein, as well as those depicted in Table 2, above.

In certain embodiments, R^(x) and R^(y) are taken together to form an optionally substituted cyclopropyl ring. In some embodiments, such compounds are of formula II-b:

or a pharmaceutically acceptable salt thereof, wherein each R¹, R², R³, R⁵, R^(a), and R^(b) is as defined in formula I and described in classes and subclasses above and herein.

In some embodiments, the R¹ group of formula II-b is optionally substituted C₃₋₇ cycloalkyl(C₁₋₃ alkyl). In some embodiments, R¹ is

In certain embodiments, the R² group of formula II-b is an optionally substituted C₃₋₇ cycloalkyl group. In certain embodiments, R² is cyclopropyl. In some embodiments, R² is hydrogen.

In some embodiments, the R⁵ group of formula II-b is an optionally substituted C₁₋₆ aliphatic group. In some embodiments, R⁵ is t-butyl.

Exemplary R³ groups of formula II-b include those described above and herein, as well as those depicted in Table 2, above.

In certain embodiments, R^(a) and R^(b) are taken together to form an oxo group. In certain embodiments, the present invention provides compounds of formula III-a or III-b:

or a pharmaceutically acceptable salt thereof, wherein each of R¹, R², R³, R⁵, and R⁷ is as defined in formula I and described in classes and subclasses above and herein.

In certain embodiments, one of R^(a) and R^(b) is hydrogen and the other is —OC(O)R′. In some embodiments, such compounds are of formula IV-a or IV-b:

or a pharmaceutically acceptable salt thereof, wherein each of R¹, R², R³, R⁵, and R⁷ is as defined in formula I and described in classes and subclasses above and herein.

In certain embodiments, the R′ group of formula IV-a and IV-b is an optionally substituted group selected from C₁₋₆ aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, or 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur. In some embodiments, R′ is substituted C₁₋₆ aliphatic. In some embodiments, R′ is trifluoromethyl.

In certain embodiments, one of R^(a) and R^(b) is hydrogen and the other is —OH. In some embodiments, such compounds are of formula V-a or V-b:

or a pharmaceutically acceptable salt thereof, wherein each of R¹, R², R³, R⁵, and R⁷ is as defined in formula I and described in classes and subclasses above and herein.

While compounds of formulae IV-a and IV-b are depicted as having unspecified stereochemistry at the carbon to which the ester group is attached, it will be understood that, in certain embodiments, compounds of formulae IV-a and IV-b may be provided having either (R) or (S) stereochemistry at this position. In certain embodiments, such compounds are of formula IV-a-1, IV-a-2, IV-b-1, or IV-b-2:

While compounds of formulae V-a and V-b, are depicted as having unspecified stereochemistry at the carbon to which the hydroxy group is attached, it will be understood that, in certain embodiments, compounds of formulae V-a and V-b may be provided having either (R) or (S) stereochemistry at this position. In certain embodiments, such compounds are of formula V-a-1, V-a-2, V-b-1, or V-b-2:

Exemplary compounds of formula I are set forth in Table 3 below.

TABLE 3 Exemplary Compounds of Formula I

I-1

I-2

I-3

I-4

I-5

I-6

I-7

I-8

I-9

I-10

I-11

I-12

I-13

I-14

I-15

I-16

I-17

I-18

I-19

I-20

I-21

I-22

I-23

In certain embodiments, the present invention provides any compound depicted in Table 3, above, or a pharmaceutically acceptable salt thereof.

As defined generally above, R³ is a warhead group. Without wishing to be bound by any particular theory, it is believed that such R³ groups, i.e. warhead groups, are particularly suitable for covalently binding to a key cysteine residue in the binding domain of HCV protease. One of ordinary skill in the art will appreciate that HCV protease, and mutants thereof, have a cysteine residue in the binding domain. In certain embodiments, compounds of the present invention have a warhead group characterized in that inventive compounds may target the C159 cysteine residue of HCV protease.

Thus, in some embodiments, R³ is characterized in that the -L-Y moiety is capable of covalently binding to a cysteine residue thereby irreversibly inhibiting the enzyme. In certain embodiments, the cysteine residue is Cys159 of HCV protease, or a mutant thereof, where the provided residue numbering is in accordance with Uniprot (code Q91RS4).

One of ordinary skill in the art will recognize that a variety of warhead groups, as defined herein, are suitable for such covalent bonding. Such R³ groups include, but are not limited to, those described herein and depicted in Table 2, supra. This phenomenon may be determined by performing mass spectroscopic experiments using the protocol described in detail in the Exemplification, infra.

According to another aspect, the present invention provides a conjugate comprising HCV protease, or a mutant thereof, covalently bonded to an inhibitor at Cys159. In some embodiments, the inhibitor is covalently bonded via a linker moiety.

In certain embodiments, the present invention provides a conjugate of the formula Cys159-linker-inhibitor moiety. One of ordinary skill in the art will recognize that the “linker” group corresponds to a —(CH₂)_(n)-L-Y warhead group as described herein. Accordingly, in certain embodiments, the linker group is as defined for —(CH₂)_(n)-L-Y was defined above and described in classes and subclasses herein. It will be appreciated, however, that the linker group is bivalent and, therefore, the corresponding —(CH₂)_(n)-L-Y group is also intended to be bivalent resulting from the reaction of the warhead with the Cys159 of HCV protease, or a mutant thereof.

In certain embodiments, the inhibitor moiety is a compound of formula A:

wherein each of the R¹, R², R⁴, R^(a), R^(b), R^(x), and R^(y) groups of formula A is as defined for formula I above and described in classes and subclasses herein. Thus, in certain embodiments, the present invention provides a conjugate of the formula:

wherein each of the R¹, R², R⁴, R^(a), R^(b), R^(x), and R^(y) groups of the conjugate is as defined for formula I above and described in classes and subclasses herein.

In some embodiments, R³ is characterized in that the -L-Y moiety is capable of covalently binding to a cysteine residue thereby irreversibly inhibiting the enzyme. In certain embodiments, the cysteine residue is Cys16 of HCV protease, or a mutant thereof, where the provided residue numbering is in accordance with Uniprot (code Q91RS4).

According to another aspect, the present invention provides a conjugate comprising HCV protease, or a mutant thereof, covalently bonded to an inhibitor at Cys16. In some embodiments, the inhibitor is covalently bonded via a linker moiety.

In certain embodiments, the present invention provides a conjugate of the formula Cys16-linker-inhibitor moiety. One of ordinary skill in the art will recognize that the “linker” group corresponds to a —(CH₂)_(n)-L-Y warhead group as described herein. Accordingly, in certain embodiments, the linker group is as defined for —(CH₂)_(n)-L-Y was defined above and described in classes and subclasses herein. It will be appreciated, however, that the linker group is bivalent and, therefore, the corresponding —(CH₂)_(n)-L-Y group is also intended to be bivalent resulting from the reaction of the warhead with the Cys16 of HCV protease, or a mutant thereof.

Thus, in certain embodiments, the present invention provides a conjugate of the formula:

wherein each of the R¹, R², R⁴, R^(a), R^(b), R^(x), and R^(y) groups of the conjugate is as defined for formula I above and described in classes and subclasses herein. General Methods of Providing the Present Compounds

In certain embodiments, the present compounds are generally prepared according to Scheme 1 set forth below.

wherein R^(3′) is selected from R³, —(CH₂)_(n)-L-H, or —(CH₂)_(n)-L-PG, each of n, L, R¹, R², and R⁵ is as defined for formula I above and described in classes and subclasses herein; and PG is as described below.

In one aspect, the present invention provides methods for preparing compounds of formula I, according to the steps depicted in Scheme 1 above wherein each variable is as defined and described herein and each PG is a suitable protecting group. At step S-1, an N-protected (e.g. Boc) ester of formula a is saponified to give a carboxylic acid of formula b. At step S-2, a carboxylic acid of formula b is condensed with a compound of formula c using peptide coupling conditions to give an alpha-hydroxy amide of formula d. Suitable peptide coupling conditions are well known in the art and include those described in detail in PCT publication number WO2002094822 (U.S. Pat. No. 6,825,347), the entirety of which is hereby incorporated by reference. Unless otherwise indicated, said conditions are referenced as suitable peptide coupling conditions throughout this application.

At step S-3, cleavage of the protective group (e.g. Boc removal) from an alpha-hydroxy amide of formula d gives an amine of formula e, or a salt thereof. In certain embodiments, cleavage of the PG group is achieved by contacting an alpha-hydroxy amide of formula d with a mineral or organic acid in a suitable solvent. In some embodiments, the acid is hydrochloric acid. In some embodiments, the solvent is dioxane.

At step S-4, an amine of formula e is coupled with a carboxylic acid of formula f using suitable peptide coupling conditions to an intermediate compound of formula g.

In some embodiments, intermediate compound of formula g is converted to compounds of formula I in steps which are described as examples herein.

In some embodiments, compounds of formula g are reacted as shown in step S-5, wherein a compound of formula g is oxidized under suitable conditions to form a compound of formula I′. In some embodiments, the suitable conditions comprise Dess-Martin periodinane.

As defined generally above, the PG group of formulae a, b, and d is a suitable amino protecting group. Suitable amino protecting groups are well known in the art and include those described in detail in Protecting Groups in Organic Synthesis, T. W. Greene and P. G. M. Wuts, 3^(rd) edition, John Wiley & Sons, 1999, the entirety of which is incorporated herein by reference. Protected amines are well known in the art and include those described in detail in Greene (1999). Suitable mono-protected amines further include, but are not limited to, aralkylamines, carbamates, allyl amines, amides, and the like. Examples of suitable mono-protected amino moieties include t-butyloxycarbonylamino (—NHBOC), ethyloxycarbonylamino, methyloxycarbonylamino, trichloroethyloxycarbonylamino, allyloxycarbonylamino (—NHAlloc), benzyloxocarbonylamino (—NHCBZ), allylamino, benzylamino (—NHBn), fluorenylmethylcarbonyl (—NHFmoc), formamido, acetamido, chloroacetamido, dichloroacetamido, trichloroacetamido, phenylacetamido, trifluoroacetamido, benzamido, t-butyldiphenylsilyl, and the like. Suitable di-protected amines include amines that are substituted with two substituents independently selected from those described above as mono-protected amines, and further include cyclic imides, such as phthalimide, maleimide, succinimide, and the like.

In other embodiments, the present compounds are generally prepared according to Scheme 1a set forth below.

wherein R^(3′) is selected from R³, —(CH₂)_(n)-L-H, or —(CH₂)_(n)-L-PG, each of n, L, R¹, R², and R⁶ is as defined for formula I above and described in classes and subclasses herein; and PG is as described below.

At step S-6, cleavage of the protective group (e.g. Boc removal) from an alpha-hydroxy amide of formula d, followed by coupling with a carboxylic acid of formula h using suitable peptide coupling conditions provides an intermediate compound of formula j.

In some embodiments, intermediate compound of formula j is converted to compounds of formula I in steps which are described as examples herein.

In some embodiments, compounds of formula j are reacted as shown in step S-7, wherein a compound of formula j is oxidized under suitable conditions to form a compound of formula I″. In some embodiments, the suitable conditions comprise Dess-Martin periodinane.

In other embodiments, the present compounds are generally prepared according to Scheme 2 set forth below.

wherein R^(3′) is selected from R³, —(CH₂)_(n)-L-H, or —(CH₂)_(n)-L-PG, each of n, L, R¹, R², R⁵, R⁶ and R⁷ is as defined for formula I above and described in classes and subclasses herein; and PG is as described below.

At step S-8, a carboxylic acid of formula k is condensed with an alpha-aminoester of formula m, or a salt thereof, using suitable peptide coupling conditions to give a carboxylic acid of formula n.

At step S-9, a carboxylic acid of formula n is condensed with an alpha-aminoester of p, or a salt thereof, using suitable peptide coupling conditions to give a carboxylic acid formula q.

At step S-10, a carboxylic acid of formula q is condensed with a proline derivative of formula r, or a salt thereof, using suitable peptide coupling conditions to give a compound of formula s.

In some embodiments, intermediate compound of formula s is converted to compounds of formula I in steps which are described as examples herein.

In some embodiments, compounds of formula s are reacted as shown in step S-11, wherein a compound of formula s is oxidized under suitable conditions to form a compound of formula I′″. In some embodiments, the suitable conditions comprise Dess-Martin periodinane.

4. Uses, Formulation and Administration

Pharmaceutically Acceptable Compositions

According to another embodiment, the invention provides a composition comprising a compound of this invention or a pharmaceutically acceptable derivative thereof and a pharmaceutically acceptable carrier, adjuvant, or vehicle. The amount of compound in compositions of this invention is such that is effective to measurably inhibit HCV protease, or a mutant thereof, in a biological sample or in a patient. In certain embodiments, the amount of compound in compositions of this invention is such that is effective to measurably inhibit HCV protease, or a mutant thereof, in a biological sample or in a patient. In certain embodiments, a composition of this invention is formulated for administration to a patient in need of such composition. In some embodiments, a composition of this invention is formulated for oral administration to a patient.

The term “patient,” as used herein, means an animal, preferably a mammal, and most preferably a human.

The term “pharmaceutically acceptable carrier, adjuvant, or vehicle” refers to a non-toxic carrier, adjuvant, or vehicle that does not destroy the pharmacological activity of the compound with which it is formulated. Pharmaceutically acceptable carriers, adjuvants or vehicles that may be used in the compositions of this invention include, but are not limited to, ion exchangers, alumina, aluminum stearate, lecithin, serum proteins, such as human serum albumin, buffer substances such as phosphates, glycine, sorbic acid, potassium sorbate, partial glyceride mixtures of saturated vegetable fatty acids, water, salts or electrolytes, such as protamine sulfate, disodium hydrogen phosphate, potassium hydrogen phosphate, sodium chloride, zinc salts, colloidal silica, magnesium trisilicate, polyvinyl pyrrolidone, cellulose-based substances, polyethylene glycol, sodium carboxymethylcellulose, polyacrylates, waxes, polyethylene-polyoxypropylene-block polymers, polyethylene glycol and wool fat.

A “pharmaceutically acceptable derivative” means any non-toxic salt, ester, salt of an ester or other derivative of a compound of this invention that, upon administration to a recipient, is capable of providing, either directly or indirectly, a compound of this invention or an inhibitorily active metabolite or residue thereof.

As used herein, the term “inhibitorily active metabolite or residue thereof” means that a metabolite or residue thereof is also an inhibitor of HCV protease, or a mutant thereof.

Compositions of the present invention may be administered orally, parenterally, by inhalation spray, topically, rectally, nasally, buccally, vaginally or via an implanted reservoir. The term “parenteral” as used herein includes subcutaneous, intravenous, intramuscular, intra-articular, intra-synovial, intrasternal, intrathecal, intrahepatic, intralesional and intracranial injection or infusion techniques. Preferably, the compositions are administered orally, intraperitoneally or intravenously. Sterile injectable forms of the compositions of this invention may be aqueous or oleaginous suspension. These suspensions may be formulated according to techniques known in the art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution or suspension in a non-toxic parenterally acceptable diluent or solvent, for example as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium.

For this purpose, any bland fixed oil may be employed including synthetic mono- or di-glycerides. Fatty acids, such as oleic acid and its glyceride derivatives are useful in the preparation of injectables, as are natural pharmaceutically-acceptable oils, such as olive oil or castor oil, especially in their polyoxyethylated versions. These oil solutions or suspensions may also contain a long-chain alcohol diluent or dispersant, such as carboxymethyl cellulose or similar dispersing agents that are commonly used in the formulation of pharmaceutically acceptable dosage forms including emulsions and suspensions. Other commonly used surfactants, such as Tweens, Spans and other emulsifying agents or bioavailability enhancers which are commonly used in the manufacture of pharmaceutically acceptable solid, liquid, or other dosage forms may also be used for the purposes of formulation.

Pharmaceutically acceptable compositions of this invention may be orally administered in any orally acceptable dosage form including, but not limited to, capsules, tablets, aqueous suspensions or solutions. In the case of tablets for oral use, carriers commonly used include lactose and corn starch. Lubricating agents, such as magnesium stearate, are also typically added. For oral administration in a capsule form, useful diluents include lactose and dried cornstarch. When aqueous suspensions are required for oral use, the active ingredient is combined with emulsifying and suspending agents. If desired, certain sweetening, flavoring or coloring agents may also be added.

Alternatively, pharmaceutically acceptable compositions of this invention may be administered in the form of suppositories for rectal administration. These can be prepared by mixing the agent with a suitable non-irritating excipient that is solid at room temperature but liquid at rectal temperature and therefore will melt in the rectum to release the drug. Such materials include cocoa butter, beeswax and polyethylene glycols.

Pharmaceutically acceptable compositions of this invention may also be administered topically, especially when the target of treatment includes areas or organs readily accessible by topical application, including diseases of the eye, the skin, or the lower intestinal tract. Suitable topical formulations are readily prepared for each of these areas or organs.

Topical application for the lower intestinal tract can be effected in a rectal suppository formulation (see above) or in a suitable enema formulation. Topically-transdermal patches may also be used.

For topical applications, provided pharmaceutically acceptable compositions may be formulated in a suitable ointment containing the active component suspended or dissolved in one or more carriers. Carriers for topical administration of compounds of this invention include, but are not limited to, mineral oil, liquid petrolatum, white petrolatum, propylene glycol, polyoxyethylene, polyoxypropylene compound, emulsifying wax and water. Alternatively, provided pharmaceutically acceptable compositions can be formulated in a suitable lotion or cream containing the active components suspended or dissolved in one or more pharmaceutically acceptable carriers. Suitable carriers include, but are not limited to, mineral oil, sorbitan monostearate, polysorbate 60, cetyl esters wax, cetearyl alcohol, 2-octyldodecanol, benzyl alcohol and water.

For ophthalmic use, provided pharmaceutically acceptable compositions may be formulated as micronized suspensions in isotonic, pH adjusted sterile saline, or, preferably, as solutions in isotonic, pH adjusted sterile saline, either with or without a preservative such as benzylalkonium chloride. Alternatively, for ophthalmic uses, the pharmaceutically acceptable compositions may be formulated in an ointment such as petrolatum.

Pharmaceutically acceptable compositions of this invention may also be administered by nasal aerosol or inhalation. Such compositions are prepared according to techniques well-known in the art of pharmaceutical formulation and may be prepared as solutions in saline, employing benzyl alcohol or other suitable preservatives, absorption promoters to enhance bioavailability, fluorocarbons, and/or other conventional solubilizing or dispersing agents.

Most preferably, pharmaceutically acceptable compositions of this invention are formulated for oral administration. Such formulations may be administered with or without food. In some embodiments, pharmaceutically acceptable compositions of this invention are administered without food. In other embodiments, pharmaceutically acceptable compositions of this invention are administered with food.

The amount of compounds of the present invention that may be combined with the carrier materials to produce a composition in a single dosage form will vary depending upon the host treated, the particular mode of administration. Preferably, provided compositions should be formulated so that a dosage of between 0.01-100 mg/kg body weight/day of the inhibitor can be administered to a patient receiving these compositions.

It should also be understood that a specific dosage and treatment regimen for any particular patient will depend upon a variety of factors, including the activity of the specific compound employed, the age, body weight, general health, sex, diet, time of administration, rate of excretion, drug combination, and the judgment of the treating physician and the severity of the particular disease being treated. The amount of a compound of the present invention in the composition will also depend upon the particular compound in the composition.

Uses of Compounds and Pharmaceutically Acceptable Compositions

Compounds and compositions described herein are generally useful for the inhibition of HCV protease activity and/or the activity of a mutant thereof. Thus, provided compounds are useful for treating non-A, non-B hepatitis, including hepatitis C.

HCV is an extremely variable virus that forms polymorphic swarms of variants within the host. Worldwide, six different genotypes have now been defined (Simmonds et al., Hepatology, Vol. 42, No. 4, 2005). These genotypes have been further classified into more closely related, genetically distinct subtypes. Comparative sequence portions, known as consensus sequences, are set forth in Table 3a, below. HCV genotypes and subtypes are distributed differently in different parts of the world, and certain genotypes predominate in certain areas. Genotypes 1-3 are widely distributed throughout the world. Subtype 1a is prevalent in North and South America, Europe, and Australia. Subtype 1b is common in North America and Europe, and is also found in parts of Asia. Genotype 2 is present in most developed countries, but is less common than genotype 1 (http://www.hcvadvocate.org/hepatitis/factsheets_pdf/genotype_FS.pdf). Other genotypes are prevalent in ex-US patient populations and are therefore important targets.

Notably, a cysteine located at amino acid position 159 in genotype 1b is conserved in all genotypes and subtypes of HCV NS3 sequenced to date, although the amino acid position may be different in other genotypes and subtypes. Targeting this cysteine residue with irreversible inhibitors should enable the development of agents which are effective against multiple HCV genotypes.

As described herein, the present invention provides irreversible inhibitors of one or more HCV protease genotypes, and variants thereof. Such compounds, comprising a warhead group designated as R³, include those of formulae I, II-a, II-b, III-a, III-b, IV-a, IV-b, V-a, V-b, IV-a-1, IV-a-2, IV-b-1, IV-b-2, V-a-1, V-a-2, V-b-1, and V-b-2, as described herein. In some embodiments, R³ is characterized in that the -L-Y moiety is capable of covalently binding to a cysteine residue thereby irreversibly inhibiting the enzyme. Without wishing to be bound by any particular theory, it is believed that such R³ groups, i.e. warhead groups, are particularly suitable for covalently binding to a key cysteine residue in the binding domain of one or more HCV protease genotypes or variants thereof. In some embodiments, one or more genotypes inhibited by compounds of the present invention include 1a, 1b, 2a, and 3a. In certain embodiments, one or more such variants include A156T, A156S, D168V, D168A, and R155K.

One of ordinary skill in the art will appreciate that HCV protease genotypes and variants thereof have one or more cysteine residues near the binding domain. Without wishing to be bound by any particular theory, it is believed that proximity of a warhead group to the cysteine of interest facilitates covalent modification of that cysteine by the warhead group. In some embodiments, the cysteine residue of interest is Cys159 of HCV protease subtype 1b, or a variant thereof, where the provided residue numbering is in accordance with Uniprot (code Q91RS4). Cysteine residues of other HCV protease genotypes and subtypes suitable for covalent modification by irreversible inhibitors of the present invention include those summarized in Table 3a, below, where the bold and underlined “C” refers to a cysteine residue conserved at an equivalent position to Cys159 of HCV protease subtype 1b.

TABLE 3a HCV genotype/ Representative Sequence subtype Sequence Portion^(a) Patient ID Identifier 1a GHAVGLFRAAV C TRGVAKAV _.H77.NC_004102 SEQ ID NO: 1 1a GHAVGIFRAAV C TRGVAKAV CH.BID-V271.EU482858 SEQ ID NO: 2 1a GHAVGIFRAAV C TRGVAKAV DE.BID-V25.EU482831 SEQ ID NO: 3 1a GHAVGLFRAAV C TRGVAKAV US.H77-H21.AF011753 SEQ ID NO: 4 1b GHAVGIFRAAV C TRGVAKAV AU.HCV-A.AJ000009 SEQ ID NO: 5 1b GHVVGIFRAAV C TRGVAKAV CH.BID-V272.EU482859 SEQ ID NO: 6 1b GHAVGIFRAAV C TRGVAKAV JP.HCV-BK.M58335 SEQ ID NO: 7 1c GHAVGIFRAAV C TRGVAKAV ID.HC-G9.D14853 SEQ ID NO: 8 1c GHVAGIFRAAV C TRGVAKAV IN.AY051292.AY051292 SEQ ID NO: 9 2a GHAVGIFRAAV C SRGVAKSI JP.AY746460.AY746460 SEQ ID NO: 10 2a GHAVGIFRAAV C SRGVAKSI JP.JCH-6.AB047645 SEQ ID NO: 11 2a GHAVGIFRAAV C SRGVAKSI _.G2AK1.AF169003 SEQ ID NO: 12 2b GHAVGLFRAAV C ARGVAKSI JP.HC-J8.D10988 SEQ ID NO: 13 2b GHAVGLFRAAV C ARGVAKSI JP.MD2b1-2.AY232731 SEQ ID NO: 14 2c GHAVGIFRAAV C SRGVAKSI _.BEBE1.D50409 SEQ ID NO: 15 2i AHAVGIFRAAV C SRGVAKSI VN.D54.DQ155561 SEQ ID NO: 16 2k GHAVGIFRAAI C TRGAAKSI MD.VAT96.AB031663 SEQ ID NO: 17 3a GHVAGIFRAAV C TRGVAKAL CH.452.DQ437509 SEQ ID NO: 18 3a GHVAGIFRAAV C TRGVAKAL DE.HCVCENS1.X76918 SEQ ID NO: 19 3a GHVAGIFRAAV C TRGVAKAL ID.ps23.EU315121 SEQ ID NO: 20 3b GHVMGIFIAVV C TRGVAKAL IN.RG416.DQ284965 SEQ ID NO: 21 3b GHVVGIFRAAV C TRGVAKAL JP.HCV-Tr.D49374 SEQ ID NO: 22 3k GHVAGIFRAAV C TRGVAKAL ID.JK049.D63821 SEQ ID NO: 23 4a GHAAGIFRAAV C TRGVAKAV EG.Eg9.DQ988077 SEQ ID NO: 24 4a GHAAGLFRAAV C TRGVAKAV _.01-09.DQ418782 SEQ ID NO: 25 4a GHAAGLFRAAV C TRGVAKAV _.F753.DQ418787 SEQ ID NO: 26 4d GHAAGIFRAAV C TRGVAKAV _.03-18.DQ418786 SEQ ID NO: 27 4d GHAAGIFRAAV C TRGVAKTV _.24.DQ516083 SEQ ID NO: 28 4f GHAVGIFRAAV C TRGVAKAV FR.IFBT84.EF589160 SEQ ID NO: 29 4f GHAVGIFRAAV C TRGVAKAV FR.IFBT88.EF589161 SEQ ID NO: 30 5a GHVVGVFRAAV C TRGVAKAL GB.EUH1480.Y13184 SEQ ID NO: 31 5a GHVVGVFRAAV C TRGVAKAL ZA.SA13.AF064490 SEQ ID NO: 32 6a GHVVGLFRAAV C TRGVAKSL HK.6a74.DQ480524 SEQ ID NO: 33 6a GHVVGLFRAAV C TRGVAKSL HK.6a77.DQ480512 SEQ ID NO: 34 6a GHVVGLFRAAV C TRGVAKSL HK.EUHK2.Y12083 SEQ ID NO: 35 6b GHVVGLFRAAV C TRGVAKAL _.Th580.NC_009827 SEQ ID NO: 36 6c GHVVGLFRAAV C TRGVAKAL TH.Th846.EF424629 SEQ ID NO: 37 6d DHVVGLFRAAV C TRGVAKAL VN.VN235.D84263 SEQ ID NO: 38 6e GHVVGLFRAAV C TRGVAKAI CN.GX004.DQ314805 SEQ ID NO: 39 6f GHAVGIFRAAV C TRGVAKAI TH.C-0044.DQ835760 SEQ ID NO: 40 6f GHAVGIFRAAV C TRGVAKAI TH.C-0046.DQ835764 SEQ ID NO: 41 6g GHVVGLFRAAV C TRGVAKAL HK.HK6554.DQ314806 SEQ ID NO: 42 6g GHVVGLFRAAV C TRGVAKAL ID.JK046.D63822 SEQ ID NO: 43 6h GHVAGIFRAAV C TRGVAKSL VN.VN004.D84265 SEQ ID NO: 44 6i GHVAGIFRAAV C TRGVAKSL TH.C-0159.DQ835762 SEQ ID NO: 45 6j GHVAGIFRAAV C TRGVAKSL TH.C-0667.DQ835761 SEQ ID NO: 46 6j GHVAGIFRAAV C TRGVAKSL TH.Th553.DQ835769 SEQ ID NO: 47 6k GHVAGIFRAAV C TRGVAKSL CN.KM41.DQ278893 SEQ ID NO: 48 6k GHVAGIFRAAV C TRGVAKSL CN.KM45.DQ278891 SEQ ID NO: 49 6k GHVAGIFRAAV C TRGVAKSL VN.VN405.D84264 SEQ ID NO: 50 6l GHVAGIFRAAV C TRGVAKSL US.537796.EF424628 SEQ ID NO: 51 6m GHAVGVFRAAV C TRGVAKSL TH.C-0185.DQ835765 SEQ ID NO: 52 6m GHAVGVFRAAV C TRGVAKSL TH.C-0208.DQ835763 SEQ ID NO: 53 6n GHVVGIFRAAV C TRGVAKSL CN.KM42.DQ278894 SEQ ID NO: 54 6n GHVVGIFRAAV C TRGVAKSL TH.D86/93.DQ835768 SEQ ID NO: 55 6o GHAVGLFRAAV C TRGVAKAI CA.QC227.EF424627 SEQ ID NO: 56 6p GHVVGLFRAAV C TRGVAKAI CA.QC216.EF424626 SEQ ID NO: 57 6q GHAVGLFRAAV C TRGVAKAI CA.QC99.EF424625 SEQ ID NO: 58 6t GHVVGLFRAAV C TRGVAKAI VN.TV241.EF632069 SEQ ID NO: 59 6t GHVVGLFRAAV C TRGVAKAI VN.TV249.EF632070 SEQ ID NO: 60 6t GHVVGLFRAAV C TRGVAKAI VN.VT21.EF632071 SEQ ID NO: 61 7a SHCVGIFRAAV C TRGVAKAV CA.QC69.EF108306 SEQ ID NO: 62 ^(a)It will be appreciated by one of ordinary skill in the art that every virus is prone to mutation and subject to polymorphisms, and any genotype consensus sequences described herein are representative of a given genotype or subtype. Such representative consensus sequences are available at http://hcv.lanl.gov/content/sequence/NEWALIGN/align.html.

Drug resistance is emerging as a significant challenge for targeted therapies. For example, drug resistance has been reported for HCV protease inhibitors in development. Such compounds include BILN 2061 and VX-950 (also known as telaprevir), developed by Boehringer Ingelheim and Vertex Pharmaceuticals, respectively. The structures of BILN 2061 and VX-950 are depicted below.

In fact, a recent article published by Vertex Pharmaceuticals, entitled, “In Vitro Resistance Studies of Hepatitis C Virus Serine Protease,” squarely addresses the problem of mutant resistance observed with VX-950 and BILN 2061. See Lin et al., The Journal of Biological Chemistry, Vol. 279, No. 17, Issue of April 23, pp. 17508-17514, 2004. This article concludes that “future hepatitis C therapy involving small molecule inhibitors of HCV enzymes might require multidrug combination, as in the case of the current HIV treatments.” See page 17513, last paragraph.

Resistance to specific antiviral drugs is a major factor limiting the efficacy of therapies against many retroviruses or RNA viruses. The error-prone nature of these viruses allows for the development of mutations that afford resistance to currently available drugs or drugs undergoing clinical testing. The resistance problem is a critical hurdle faced in drug development of new HCV-specific inhibitors to treat HCV patients.

A recent in vitro resistance study using two HCV NS3.4A protease inhibitors, VX-950 and BILN 2061, found that resistance mutations selected against either inhibitor resulted in a significant reduction in susceptibility to the inhibitor itself. However, the primary resistance mutations against BILN 2061 were fully susceptible to VX-950, and the major resistance mutation against VX-950 remained sensitive to BILN 2061 (Lin et al., Jour. Biol. Chem. 279(17): 17508-14, 2004).

In the ensuing Examples, provided compounds of the present invention have an HCV activity profile reflecting inhibition of several HCV protease mutants.

As used herein, the term “clinical drug resistance” refers to the loss of susceptibility of a drug target to drug treatment as a consequence of mutations in the drug target

As used herein, the term “resistance” refers to changes in the wild-type nucleic acid sequence coding a target protein, and/or the protein sequence of the target, which changes decrease or abolish the inhibitory effect of the inhibitor on the target protein.

Examples of proteases that are inhibited by the compounds and compositions described herein and against which the methods described herein are useful include NS3, NS3.4A, or a mutant thereof.

The activity of a compound utilized in this invention as an inhibitor of NS3, NS3.4A, or a mutant thereof, may be assayed in vitro, in vivo or in a cell line. In vitro assays include assays that determine inhibition of either the serine protease activity and/or the subsequent functional consequences, or ATPase activity of activated NS3, NS3.4A, or a mutant thereof. Alternate in vitro assays quantitate the ability of the inhibitor to bind to NS3 or NS3.4A. Inhibitor binding may be measured by radiolabelling the inhibitor prior to binding, isolating the inhibitor/NS3 or inhibitor/NS3.4A complex and determining the amount of radiolabel bound. Alternatively, inhibitor binding may be determined by running a competition experiment where new inhibitors are incubated with NS3 or NS3.4A bound to known radioligands. Detailed conditions for assaying a compound utilized in this invention as an inhibitor of NS3 or NS3.4A, or a mutant thereof, are set forth in the Examples below.

Serine proteases are a large family of proteolytic enzymes that cleave peptide bonds in proteins. The serine protease family includes the digestive enzymes chymotrypsin, trypsin, and elastase, and proteases involved in blood clotting. Serine proteases possess a characteristic “catalytic triad” comprising serine, aspartic acid, and histidine, that together function to activate serine to form a covalent bond with the enzyme substrate, thereby hydrolyzing a peptide bond. In addition to those stated above, serine proteases participate in a variety of functions including immunity and inflammation.

As used herein, the terms “treatment,” “treat,” and “treating” refer to reversing, alleviating, delaying the onset of, or inhibiting the progress of a disease or disorder, or one or more symptoms thereof, as described herein. In some embodiments, treatment may be administered after one or more symptoms have developed. In other embodiments, treatment may be administered in the absence of symptoms. For example, treatment may be administered to a susceptible individual prior to the onset of symptoms (e.g., in light of a history of symptoms and/or in light of genetic or other susceptibility factors). Treatment may also be continued after symptoms have resolved, for example to prevent or delay their recurrence.

The compounds and compositions, according to the method of the present invention, may be administered using any amount and any route of administration effective for treating or lessening the severity of cancer, an autoimmune disorder, a neurodegenerative or neurological disorder, schizophrenia, a bone-related disorder, liver disease, or a cardiac disorder. The exact amount required will vary from subject to subject, depending on the species, age, and general condition of the subject, the severity of the infection, the particular agent, its mode of administration, and the like. The compounds of the invention are preferably formulated in dosage unit form for ease of administration and uniformity of dosage. The expression “dosage unit form” as used herein refers to a physically discrete unit of agent appropriate for the patient to be treated. It will be understood, however, that the total daily usage of the compounds and compositions of the present invention will be decided by the attending physician within the scope of sound medical judgment. The specific effective dose level for any particular patient or organism will depend upon a variety of factors including the disorder being treated and the severity of the disorder; the activity of the specific compound employed; the specific composition employed; the age, body weight, general health, sex and diet of the patient; the time of administration, route of administration, and rate of excretion of the specific compound employed; the duration of the treatment; drugs used in combination or coincidental with the specific compound employed, and like factors well known in the medical arts. The term “patient”, as used herein, means an animal, preferably a mammal, and most preferably a human.

The pharmaceutically acceptable compositions of this invention can be administered to humans and other animals orally, rectally, parenterally, intracisternally, intravaginally, intraperitoneally, topically (as by powders, ointments, or drops), bucally, as an oral or nasal spray, or the like, depending on the severity of the infection being treated. In certain embodiments, the compounds of the invention may be administered orally or parenterally at dosage levels of about 0.01 mg/kg to about 50 mg/kg and preferably from about 1 mg/kg to about 25 mg/kg, of subject body weight per day, one or more times a day, to obtain the desired therapeutic effect.

In some embodiments, a provided composition is administered to a patient in need thereof once daily. Without wishing to be bound by any particular theory, it is believed that prolonged duration of action of an irreversible inhibitor of HCV NS3 protease is particularly advantageous for once daily administration to a patient in need thereof for the treatment of a disorder associated with HCV NS3 protease. In certain embodiments, a provided composition is administered to a patient in need thereof at least once daily. In other embodiments, a provided composition is administered to a patient in need thereof twice daily, three times daily, or four times daily.

Liquid dosage forms for oral administration include, but are not limited to, pharmaceutically acceptable emulsions, microemulsions, solutions, suspensions, syrups and elixirs. In addition to the active compounds, the liquid dosage forms may contain inert diluents commonly used in the art such as, for example, water or other solvents, solubilizing agents and emulsifiers such as ethyl alcohol, isopropyl alcohol, ethyl carbonate, ethyl acetate, benzyl alcohol, benzyl benzoate, propylene glycol, 1,3-butylene glycol, dimethylformamide, oils (in particular, cottonseed, groundnut, corn, germ, olive, castor, and sesame oils), glycerol, tetrahydrofurfuryl alcohol, polyethylene glycols and fatty acid esters of sorbitan, and mixtures thereof. Besides inert diluents, the oral compositions can also include adjuvants such as wetting agents, emulsifying and suspending agents, sweetening, flavoring, and perfuming agents.

Injectable preparations, for example, sterile injectable aqueous or oleaginous suspensions may be formulated according to the known art using suitable dispersing or wetting agents and suspending agents. The sterile injectable preparation may also be a sterile injectable solution, suspension or emulsion in a nontoxic parenterally acceptable diluent or solvent, for example, as a solution in 1,3-butanediol. Among the acceptable vehicles and solvents that may be employed are water, Ringer's solution, U.S.P. and isotonic sodium chloride solution. In addition, sterile, fixed oils are conventionally employed as a solvent or suspending medium. For this purpose any bland fixed oil can be employed including synthetic mono- or diglycerides. In addition, fatty acids such as oleic acid are used in the preparation of injectables.

The injectable formulations can be sterilized, for example, by filtration through a bacterial-retaining filter, or by incorporating sterilizing agents in the form of sterile solid compositions which can be dissolved or dispersed in sterile water or other sterile injectable medium prior to use.

In order to prolong the effect of a compound of the present invention, it is often desirable to slow the absorption of the compound from subcutaneous or intramuscular injection. This may be accomplished by the use of a liquid suspension of crystalline or amorphous material with poor water solubility. The rate of absorption of the compound then depends upon its rate of dissolution that, in turn, may depend upon crystal size and crystalline form. Alternatively, delayed absorption of a parenterally administered compound form is accomplished by dissolving or suspending the compound in an oil vehicle. Injectable depot forms are made by forming microencapsule matrices of the compound in biodegradable polymers such as polylactide-polyglycolide. Depending upon the ratio of compound to polymer and the nature of the particular polymer employed, the rate of compound release can be controlled. Examples of other biodegradable polymers include poly(orthoesters) and poly(anhydrides). Depot injectable formulations are also prepared by entrapping the compound in liposomes or microemulsions that are compatible with body tissues.

Compositions for rectal or vaginal administration are preferably suppositories which can be prepared by mixing the compounds of this invention with suitable non-irritating excipients or carriers such as cocoa butter, polyethylene glycol or a suppository wax which are solid at ambient temperature but liquid at body temperature and therefore melt in the rectum or vaginal cavity and release the active compound.

Solid dosage forms for oral administration include capsules, tablets, pills, powders, and granules. In such solid dosage forms, the active compound is mixed with at least one inert, pharmaceutically acceptable excipient or carrier such as sodium citrate or dicalcium phosphate and/or a) fillers or extenders such as starches, lactose, sucrose, glucose, mannitol, and silicic acid, b) binders such as, for example, carboxymethylcellulose, alginates, gelatin, polyvinylpyrrolidinone, sucrose, and acacia, c) humectants such as glycerol, d) disintegrating agents such as agar-agar, calcium carbonate, potato or tapioca starch, alginic acid, certain silicates, and sodium carbonate, e) solution retarding agents such as paraffin, f) absorption accelerators such as quaternary ammonium compounds, g) wetting agents such as, for example, cetyl alcohol and glycerol monostearate, h) absorbents such as kaolin and bentonite clay, and i) lubricants such as talc, calcium stearate, magnesium stearate, solid polyethylene glycols, sodium lauryl sulfate, and mixtures thereof. In the case of capsules, tablets and pills, the dosage form may also comprise buffering agents.

Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polyethylene glycols and the like. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings and other coatings well known in the pharmaceutical formulating art. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes. Solid compositions of a similar type may also be employed as fillers in soft and hard-filled gelatin capsules using such excipients as lactose or milk sugar as well as high molecular weight polethylene glycols and the like.

The active compounds can also be in micro-encapsulated form with one or more excipients as noted above. The solid dosage forms of tablets, dragees, capsules, pills, and granules can be prepared with coatings and shells such as enteric coatings, release controlling coatings and other coatings well known in the pharmaceutical formulating art. In such solid dosage forms the active compound may be admixed with at least one inert diluent such as sucrose, lactose or starch. Such dosage forms may also comprise, as is normal practice, additional substances other than inert diluents, e.g., tableting lubricants and other tableting aids such a magnesium stearate and microcrystalline cellulose. In the case of capsules, tablets and pills, the dosage forms may also comprise buffering agents. They may optionally contain opacifying agents and can also be of a composition that they release the active ingredient(s) only, or preferentially, in a certain part of the intestinal tract, optionally, in a delayed manner. Examples of embedding compositions that can be used include polymeric substances and waxes.

Dosage forms for topical or transdermal administration of a compound of this invention include ointments, pastes, creams, lotions, gels, powders, solutions, sprays, inhalants or patches. The active component is admixed under sterile conditions with a pharmaceutically acceptable carrier and any needed preservatives or buffers as may be required. Ophthalmic formulation, ear drops, and eye drops are also contemplated as being within the scope of this invention. Additionally, the present invention contemplates the use of transdermal patches, which have the added advantage of providing controlled delivery of a compound to the body. Such dosage forms can be made by dissolving or dispensing the compound in the proper medium. Absorption enhancers can also be used to increase the flux of the compound across the skin. The rate can be controlled by either providing a rate controlling membrane or by dispersing the compound in a polymer matrix or gel.

According to one embodiment, the invention relates to a method of inhibiting serine protease activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound.

According to another embodiment, the invention relates to a method of inhibiting HCV protease, or a mutant thereof, activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound. In certain embodiments, the invention relates to a method of irreversibly inhibiting HCV protease, or a mutant thereof, activity in a biological sample comprising the step of contacting said biological sample with a compound of this invention, or a composition comprising said compound.

The term “biological sample”, as used herein, includes, without limitation, cell cultures or extracts thereof; biopsied material obtained from a mammal or extracts thereof; and blood, saliva, urine, feces, semen, tears, or other body fluids or extracts thereof.

Inhibition of HCV protease, or a mutant thereof, activity in a biological sample is useful for a variety of purposes that are known to one of skill in the art. Examples of such purposes include, but are not limited to, blood transfusion, organ-transplantation, biological specimen storage, and biological assays.

Another embodiment of the present invention relates to a method of inhibiting HCV protease, or a mutant thereof, activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound.

According to another embodiment, the invention relates to a method of inhibiting HCV protease, or a mutant thereof, activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound. According to certain embodiments, the invention relates to a method of irreversibly inhibiting HCV protease, or a mutant thereof, activity in a patient comprising the step of administering to said patient a compound of the present invention, or a composition comprising said compound. In other embodiments, the present invention provides a method for treating a disorder mediated by HCV protease, or a mutant thereof, in a patient in need thereof, comprising the step of administering to said patient a compound according to the present invention or pharmaceutically acceptable composition thereof. Such disorders are described in detail herein.

Depending upon the particular condition, or disease, to be treated, additional therapeutic agents, which are normally administered to treat that condition, may be administered in combination with compounds and compositions of this invention. As used herein, additional therapeutic agents that are normally administered to treat a particular disease, or condition, are known as “appropriate for the disease, or condition, being treated”.

In certain embodiments, a provided compound, or composition thereof, is administered in combination with another inhibitor of HCV protease, or a variant thereof. In some embodiments, a provided compound, or composition thereof, is administered in combination with another antiviral agent. Such antiviral agents include, but are not limited to, immunomodulatory agents, such as α-, β-, and γ-interferons, pegylated derivatized interferon-α compounds, and thymosin; other anti-viral agents, such as ribavirin, amantadine, and telbivudine; other inhibitors of hepatitis C proteases (NS2-NS3 inhibitors and NS3-NS4A inhibitors, e.g. BILN 2061 and VX-950); inhibitors of other targets in the HCV life cycle, including helicase and polymerase inhibitors; inhibitors of internal ribosome entry; broad-spectrum viral inhibitors, such as IMPDH inhibitors (e.g., mycophenolic acid and derivatives thereof); or combinations of any of the above.

In certain embodiments, a combination of 2 or more antiviral agents may be administered. In certain embodiments, a combination of 3 or more antiviral agents may be administered. In some embodiments, the antiviral agents are selected from ribavirin or interferon. In other embodiments, the antiviral agent is α-interferon.

Other examples of agents the inhibitors of this invention may also be combined with include, without limitation: treatments for Alzheimer's Disease such as Aricept® and Excelon®; treatments for HIV such as ritonavir; treatments for Parkinson's Disease such as L-DOPA/carbidopa, entacapone, ropinrole, pramipexole, bromocriptine, pergolide, trihexephendyl, and amantadine; agents for treating Multiple Sclerosis (MS) such as beta interferon (e.g., Avonex® and Rebie), Copaxone®, and mitoxantrone; treatments for asthma such as albuterol and Singulair®; agents for treating schizophrenia such as zyprexa, risperdal, seroquel, and haloperidol; anti-inflammatory agents such as corticosteroids, TNF blockers, IL-1 RA, azathioprine, cyclophosphamide, and sulfasalazine; immunomodulatory and immunosuppressive agents such as cyclosporin, tacrolimus, rapamycin, mycophenolate mofetil, interferons, corticosteroids, cyclophophamide, azathioprine, and sulfasalazine; neurotrophic factors such as acetylcholinesterase inhibitors, MAO inhibitors, interferons, anti-convulsants, ion channel blockers, riluzole, and anti-Parkinsonian agents; agents for treating cardiovascular disease such as beta-blockers, ACE inhibitors, diuretics, nitrates, calcium channel blockers, and statins; agents for treating liver disease such as corticosteroids, cholestyramine, interferons, and anti-viral agents; agents for treating blood disorders such as corticosteroids, anti-leukemic agents, and growth factors; agents that prolong or improve pharmacokinetics such as cytochrome P450 inhibitors (i.e., inhibitors of metabolic breakdown) and CYP3A4 inhibitors (e.g., ketokenozole and ritonavir), and agents for treating immunodeficiency disorders such as gamma globulin.

In certain embodiments, compounds of the present invention, or a pharmaceutically acceptable composition thereof, are administered in combination with a monoclonal antibody or an siRNA therapeutic.

Those additional agents may be administered separately from an inventive compound-containing composition, as part of a multiple dosage regimen. Alternatively, those agents may be part of a single dosage form, mixed together with a compound of this invention in a single composition. If administered as part of a multiple dosage regime, the two active agents may be submitted simultaneously, sequentially or within a period of time from one another normally within five hours from one another.

As used herein, the term “combination,” “combined,” and related terms refers to the simultaneous or sequential administration of therapeutic agents in accordance with this invention. For example, a compound of the present invention may be administered with another therapeutic agent simultaneously or sequentially in separate unit dosage forms or together in a single unit dosage form. Accordingly, the present invention provides a single unit dosage form comprising a compound of formula I, an additional therapeutic agent, and a pharmaceutically acceptable carrier, adjuvant, or vehicle.

The amount of both, an inventive compound and additional therapeutic agent (in those compositions which comprise an additional therapeutic agent as described above) that may be combined with the carrier materials to produce a single dosage form will vary depending upon the host treated and the particular mode of administration. Preferably, compositions of this invention should be formulated so that a dosage of between 0.01-100 mg/kg body weight/day of an inventive can be administered.

In those compositions which comprise an additional therapeutic agent, that additional therapeutic agent and the compound of this invention may act synergistically. Therefore, the amount of additional therapeutic agent in such compositions will be less than that required in a monotherapy utilizing only that therapeutic agent. In such compositions a dosage of between 0.01-100 mg/kg body weight/day of the additional therapeutic agent can be administered.

The amount of additional therapeutic agent present in the compositions of this invention will be no more than the amount that would normally be administered in a composition comprising that therapeutic agent as the only active agent. Preferably the amount of additional therapeutic agent in the presently disclosed compositions will range from about 50% to 100% of the amount normally present in a composition comprising that agent as the only therapeutically active agent.

EXEMPLIFICATION

As depicted in the Examples below, in certain exemplary embodiments, compounds are prepared according to the following general procedures. It will be appreciated that, although the general methods depict the synthesis of certain compounds of the present invention, the following general methods, and other methods known to one of ordinary skill in the art, can be applied to all compounds and subclasses and species of each of these compounds, as described herein.

Compound numbers utilized in the Examples, below, correspond to compound numbers set forth in Table 3, supra.

Example 1

(1R,2S,5S)-3-((S)-3-acrylamido-2-(3-tert-butylureido)propanoyl)-N-(4-amino-1-cyclobutyl-3,4-dioxobutan-2-yl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide [I-1]

The title compound was prepared according to the steps and intermediates as described below.

Step 1a: Intermediate 1a

To a solution of (1R,2S,5S)-3-tert-butyl 2-methyl 6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2,3-dicarboxylate (0.30 g, 1.1 mmol) in 4 mL THF/MeOH (1:1) was added 1 N aqueous LiOH solution (2.0 mL). After stirring at r.t. for 10 hours, the reaction mixture was neutralized with 1.0 N HCl. The organic solvents were evaporated under vacuum, and the remaining aqueous phase was acidified to pH-3 using 1.0 N HCl and was extracted with EtOAc. The organic layer was washed with brine, and was dried over anhydrous magnesium sulfate. After removal of solvent, 0.28 g of Intermediate 1a was obtained: MS m/z: 254.2 (ES−).

Step 1b: Intermediate 1b

To a solution of the product of step 1a (0.28 g, 1.0 mmol) and 3-amino-4-cyclobutyl-2-hydroxybutanamide (0.27 g, 1.3 mmol) in 10.0 ml of anhydrous acetonitrile was added HATU (0.45 g, 1.2 mmol) and DIEA (0.5 ml, 3.0 mmol) at r.t. under stirring. TLC analysis indicated completion of the coupling reaction had occurred after 10 hours. A 50-ml portion of EtOAc was added in and the mixture was washed with aqueous NaHCO₃ and brine. The organic layer was separated and was dried over Na₂SO₄. After removal of solvent, the crude product was subject to chromatography on silica gel (eluents: EtOAc/hexane). A total of 0.4 g of the title compound was obtained (88%). MS m/z: 432.2 (ES+, M+Na).

Step 1c: Intermediate 1c

The product from step 1b (0.40 g, 1.0 mmol) was dissolved in 5 mL 4 N HCl in dioxane. The mixture was stirred at r.t. for 1 hour. After removal of solvents, a 10-mL portion of DCM was poured in followed by evaporation to dryness. This process of DCM addition followed by evaporation was repeated four times to give a residue solid which was used directly for the next step: MS m/z: 310.1 (M+H⁺).

Step 1d: Intermediate 1d

To a solution of the product from step 1c (0.10 g, 0.28 mmol) and (S)-3-(tert-butoxycarbonylamino)-2-(3-tert-butylureido)propanoic acid (0.10 g, 0.33 mmol) in 3.0 mL of anhydrous acetonitrile was added HATU (125 mg, 0.33 mmol) and DIEA (0.17 mL, 1.0 mmol) at r.t. under stirring. After one hour, 15 mL of EtOAc was added in and the mixture was washed with aqueous NaHCO₃ and brine. The organic layer was separated and was dried over Na₂SO₄. After removal of solvent, the crude product was subject to chromatography on silica gel (eluents: EtOAc/hexane) to afford 103 mg of the title compound (60%). MS m/z: 595.2 (M+H⁺).

Step 1e: Intermediate 1e

The product from step 1d (75 mg, 0.12 mmol) was dissolved in 3 mL of 4 N HCl in dixoxane and the reaction was stirred for 1 hour at RT. After removal of solvents, a 3-mL portion of DCM was poured in followed by evaporation to dryness. This process of DCM addition followed by evaporation was repeated three times to give a light brown solid and was used directly for the next step. MS m/z: 495.2 (M+H⁺).

Step 1f: Intermediate 1f

Acrylic acid (13.6 mg, 0.19 mmol) was coupled with the product from step 1e with HATU (65 mg, 0.17 mmol) following the procedure described in step 1b to afford the title compound (60 mg, crude). MS m/z: 549.3 (M+H⁺).

Step 1g: (1R,2S,5S)-3-((S)-3-acrylamido-2-(3-tert-butylureido)propanoyl)-N-(4-amino-1-cyclobutyl-3,4-dioxobutan-2-yl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexane-2-carboxamide

The crude product from step 1f (60 mg, 0.11 mmol) was dissolved in 5 ml of dichloromethane followed by the addition of the Dess-Martin periodinane (60 mg, 0.15 mmol). The resulting solution was stirred for 1 h at room temperature. The solvent was then removed and the residue was subject to chromatography on silica gel (eluents: EtOAc/Heptanes) to provide 13 mg of the title compound. MS m/z: 547.2 (M+H⁺).

In similar fashion using the product of step 1e (Intermediate 1e), coupling with vinylsulfonylchloride followed by oxidation using the procedures described in step 1f and 1g, the following compound can be prepared:

Following the procedures described in example 1, using (S)-4-(tert-butoxycarbonylamino)-2-(3-tert-butylureido)butanoic acid to couple with intermediate 1c in step 1d, the following compound can be prepared:

In similar fashion, using (S)-4-(tert-butoxycarbonylamino)-2-(3-tert-butylureido)butanoic acid to couple with intermediate 1c in step 1d, de-Boc following step 1e, then coupling with vinylsulfonylchloride followed by oxidation using the procedures described in step 1f and 1g, the following compound can be prepared:

Following the procedures described in example 1, using hydroxyl protected (S)-2-(3-tert-butylureido)-3-hydroxypropanoic acid to couple with intermediate 1c in step 1d, and using crotyl chloride in step 1f, the following compound can be prepared:

Example 2

tert-butyl (S)-1-((1R,2S,5S)-2-(4-amino-1-cyclobutyl-3,4-dioxobutan-2-ylcarbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl)-7-methyl-1,5-dioxooct-6-en-2-ylcarbamate [I-6]

The title compound was prepared according to the steps and intermediates as described below.

Step 2a: Intermediate 2a

To a solution of N-Boc-pyroglutamic acid (0.23 g 1.0 mmol) in 10.0 mL of anhydrous THF was added 2-methylprop-1-enyl)magnesium bromide (0.5 M in THF, 5 mL, 2.5 mmol) at −78° C. slowly. The reaction mixture was stirred for 1 h at −78° C. 1 N HCl (2.5 ml) aqueous solution was added and the mixture was slowly warmed up to RT. The pH was adjusted to ˜3-4 with 1 N HCl. The THF was then removed under vacuum and the remaining aqueous was extracted by DCM (3×15 ml). The organic layer was dried over Na₂SO₄, filtered and the solvent was removed to provide the crude product.

Step 2b: Intermediate 2b

The title compound was made by coupling Intermediate 1c from Example 1 and Intermediate 2a using HATU following the coupling reaction described for Intermediate 1b in Example 1. A total of 100 mg of the title compound (crude) was obtained from 120 mg of Intermediate 1c. MS m/z: 599.3 (M+Na⁺).

Step 2c: tert-butyl (S)-1-((1R,2S,5S)-2-(4-amino-1-cyclobutyl-3,4-dioxobutan-2-ylcarbamoyl)-6,6-dimethyl-3-azabicyclo[3.1.0]hexan-3-yl)-7-methyl-1,5-dioxooct-6-en-2-ylcarbamate

The crude product from step 2b (100 mg, 0.15 mmol) was dissolved in 5 mL of dichloromethane followed by the addition of the Dess-Martin periodinane (150 mg, 0.36 mmol). The resulting solution was stirred for 1 h at room temperature. The solvent was then removed and the residue was subject to chromatography on silica gel (eluents: EtOAc/Heptanes) to provide 60 mg of the title compound. MS m/z: 575.3 (M+H⁺).

Starting from the Intermediate 1c, by coupling with the appropriate intermediates made similarly as described in Step 2a, the following compounds are prepared:

Example 3

(1S,3aR,6aS)-2-((S)-3-acrylamido-2-((S)-2-cyclohexyl-2-(pyrazine-2-carboxamido)acetamido)propanoyl)-N—((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide [I-11]

The title compound was prepared according to the steps and intermediates as described below.

Step 3a: Intermediate 3a

To a stirring solution of 372 mg of pyrazine-2-carboxylic acid (3 mmol), 623 mg of (5)-methyl 2-amino-2-cyclohexylacetate (3 mmol), and 2.5 mL of N,N-diisopropyl ethylamine in 25 mL of anhydrous dichloromethane, was added 760 mg of 1,4-dimethyl-2-chloroimidazolium hydrochloride (4.5 mmol) in three portions. The resulting mixture was stirred at RT for additional 30 min, then concentrated under reduced pressure. The residue was re-dissolved into 80 mL of ethyl acetate, and washed with aqueous sodium bicarbonate, brine, and dried over anhydrous sodium sulfate. After concentration, the crude product was purified by flash column chromatography, eluting with heptane/ethyl acetate (v/v 2/1), giving 897 mg of yellowish oil as desired ester.

To a stirring solution of the ester obtained above in 4 mL of MeOH and 4 mL of THF, was added 6 mL of 2.0 N LiOH aqueous solution. The mixture was stirred at RT overnight, then 12 mL of 1.0 N aqueous HCl added. The reaction mixture was extracted with dichloromethane 50 mL×2, and dried over anhydrous MgSO₄. After filtration, the filtrate was concentrated to give 700 mg of the title compound.

¹H NMR (CDCl₃, 400 MHz) δ 9.40 (d, 1H, J=1.4 Hz), 8.78 (d, 1H, J=2.2 Hz), 8.58 (d, 1H, J=1.0 Hz), 8.25 (d, 1H, J=8.4 Hz), 4.78 (dd, 1H, J=4.8, 8.4 Hz), 2.05 (m, 1H), 1.80 (m, 4H), 1.78 (m, 1H), 1.10-1.35 (m, 5H).

Step 3b: Intermediate 3b

To a stirring mixture of 263 mg of the product from step 3a (1 mmol), 254 mg of (S)-methyl 2-amino-3-(tert-butoxycarbonylamino)propanoate hydrochloride (1 mmol), 1 mL of N,N-diisopropyl ethylamine in 10 mL of acetonitrile, was added 450 mg of HATU (1.2 mmol). The reaction mixture was stirred at RT overnight, then suspended in 60 mL of EtOAc and 15 mL of saturated NaHCO₃. The organic layer was separated and washed with 10 mL of 1 N HCl, 15 mL of brine, dried over Na₂SO₄. After concentration, the residue was purified by flash column chromatography on silica gel, giving 463 mg of desired ester.

To a stirring solution of 463 mg of ester in 10 mL of THF and 10 mL of MeOH, was added 10 ml, of 1.0 N LiOH aqueous solution. The reaction mixture was stirred at RT for 30 min, LC-MS showed completion of ester hydrolysis. The solvent was removed under reduced pressure, and the residue was extracted with 80 mL of dichloromethane. The organic layer was washed with 20 mL of brine and dried with MgSO4. After concentration, the title compound was obtained as white solid in quantitative yield.

LC-MS: 448.2 (ES−)

Step 3c: Intermediate 3c

To a mixture of 255 mg of (1S,3aR,6aS)-2-(tert-butoxycarbonyl)octahydrocyclopenta[c]pyrrole-1-carboxylic acid (1 mmol), 186 mg of (S)-3-amino-N-cyclopropyl-2-hydroxyhexanamide (1 mmol), and 1.0 mL of N,N-diisopropyl ethylamine in 10 mL of acetonitrile, was added 400 mg of HATU (1.05 mmol). After 16 hr, the mixture was diluted with 50 mL of EtOAc, and washed with aqueous NaHCO₃ 15 mL, 1 N aqueous HCl 10 mL, brine 10 mL, and dried over Na₂SO₄. After concentration, the residue was purified by flash column chromatography on silica gel (eluent 25% heptanes in EtOAc), giving 410 mg of desired amide as white solid.

The Boc group of the amide obtained above was removed by stirring in 6 mL of 4.0 M HCl in dioxane for 30 min. The solvent was then evaporated under reduced pressure, and the residue was dried in vacuum giving 350 mg of white solid as desired product.

LC-MS: 324.2 (ES+)

Step 3d: Intermediate 3d

To a mixture of 274 mg of the product from step 3b (0.61 mmol), 220 mg of the product from step 3c (0.61 mmol), and 1.5 mL of N,N-diisopropyl ethylamine in 8 mL of acetonitrile, was added 300 mg of HATU (0.8 mmol). After 1 hr, the mixture was diluted with 100 mL of EtOAc, and washed with aqueous NaHCO₃ 15 mL, 1 N aqueous HCl 10 mL, brine 10 mL, and dried over Na₂SO₄. After concentration, the residue was purified by flash column chromatography on silica gel (eluent 5% MeOH in EtOAc), giving 440 mg of desired amide as yellowish syrup (95%).

LC-MS: 753.4 (ES−)

Step 3e: Intermediate 3e

The title compound (217 mg, 53%) was prepared from the product of step 3d following the procedures described in step 1e and 1f.

LC-MS: 709.3 (ES+), 707.3 (ES−)

Step 3f: (1S,3aR,6aS)-2-((S)-3-acrylamido-2-((S)-2-cyclohexyl-2-(pyrazine-2-carboxamido)acetamido)propanoyl)-N—((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide

To a stirring mixture of 217 mg of the product of step 3e (0.306 mmol) in 15 mL of dichloromethane, was added 390 mg of Dess-martin reagent (0.92 mmol). After 1 hr, LC-MS showed complete conversion. 15 mL of saturated NaHCO₃ was added, and the stirring was continued for another 1 hr. The organic layer was separated, and the aqueous layer was extracted one more time with 30 mL of dichloromethane. The combined organic layer was washed with 20 mL of brine, and dried over MgSO₄. After filtration and concentration, the residue was purified by Pre-HPLC using 0.1% TFA as modifier in water and acetonitrile, giving 45 mg of the title compound.

LC-MS: 707.3 (ES+), 705.3 (ES−)

In similar fashion starting from the product of step 3d (Intermediate 3d), following the procedures described in step 3e and 3f (the de-boc, coupling and oxidation sequences), by using vinylsulfonylchloride in place of acrylic acid and HATU, the following compound can be prepared:

Following the procedures described in example 3, using (S)-4-(tert-butoxycarbonylamino)-2-(3-tert-butylureido)butanoic acid to couple with intermediate 3a in step 3b, the following compound can be prepared:

In similar fashion, using (S)-4-(tert-butoxycarbonylamino)-2-(3-tert-butylureido)butanoic acid in step 3b, and using vinylsulfonylchloride in step 3e following the procedures described in example 3, the following compound can be prepared:

Example 4

tert-butyl-(S)-1-((1S,3aR,6aS)-1-((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-ylcarbamoyl)hexahydrocyclopenta[c]pyrrol-2(1H)-yl)-7-methyl-1,5-dioxooct-6-en-2-ylcarbamate

The title compound is prepared according to the steps and intermediates as described below.

Step 4a: Intermediate 4a

The title compound is prepared by coupling intermediate 2a and intermediate 3c following the procedure described in step 2b in example 2.

Step 4b: tert-butyl (S)-1-((1S,3aR,6aS)-1-((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-ylcarbamoyl)hexahydrocyclopenta[c]pyrrol-2(1H)-yl)-7-methyl-1,5-dioxooct-6-en-2-ylcarbamate

The product from step 4a is oxidized to afford the title compound following the procedure described in step 2c in example 2.

Starting from the Intermediate 3c, by coupling with the appropriate intermediates made similarly as described in Step 2a, the following compounds are prepared:

Example 5

(1S,3aR,6aS)-2-((S)-2-((S)-2-cyclohexyl-2-(pyrazine-2-carboxamido)acetamido)-7-methyl-5-oxooct-6-enoyl)-N—((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide

The title compound is prepared according to the steps and intermediates as described below.

Step 5a: Intermediate 5a

The product from step 4a is treated with 4N HCl to afford the title compound following the procedure described in step 1c in example 1.

Step 5b: Intermediate 5b

Intermediate 3a is coupled with Intermediate 5a with HATU following the procedure described in step 3d in example 3 to produce the title compound.

Step 5c: (1S,3aR,6aS)-2-((S)-2-((S)-2-cyclohexyl-2-(pyrazine-2-carboxamido)acetamido)-7-methyl-5-oxooct-6-enoyl)-N—((S)-1-(cyclopropylamino)-1,2-dioxohexan-3-yl)octahydrocyclopenta[c]pyrrole-1-carboxamide

The product from step 5b is oxidized to afford the title compound following the procedure described in step 3f in example 3.

In similar fashion, the following compounds are prepared:

Example 6

(S)-3-((1S,3aR,6aS)-2-((S)-3-acrylamido-2-((S)-2-cyclohexyl-2-(pyrazine-2-carboxamido)acetamido)propanoyl)octahydrocyclopenta[c]pyrrole-1-carboxamido)-1-(cyclopropylamino)-1-oxohexan-2-yl 2,2,2-trifluoroacetate, [I-23]

The title compound was prepared following steps 3a to 3e, by using (S)-3-amino-1-(cyclopropylamino)-1-oxohexan-2-yl 2,2,2-trifluoroacetate in step 3c in place of (S)-3-amino-N-cyclopropyl-2-hydroxyhexanamide.

LC-MS: 805.3 (ES+)

Example 7 Single Chain HCV Protease (wt) Peptide Expression and Purification

The single-chain proteolytic domain (NS4A₂₁₋₃₂-GSGS-NS₃₃₋₆₃₁) was cloned into pET-14b (Novagen, Madison, Wis.) and transformed into DH10B cells (Invitrogen). The resulting plasmid was transferred into Escherichia coli BL21 (Novagen) for protein expression and purification as described previously (1, 2). Briefly, the cultures were grown at 37° C. in LB medium containing 100 μg/mL of ampicillin until the optical density at 600 nm (OD600) reached 1.0 and were induced by addition of isopropyl-β-D-thiogalactopyranoside (IPTG) to 1 mM. After an additional incubation at 18° C. for 20 h, bacteria were harvested by centrifugation at 6,000×g for 10 min and resuspended in a lysis buffer containing 50 mM Na₃PO₄, pH 8.0, 300 mM NaCl, 5 mM 2-mercaptoethanol, 10% glycerol, 0.5% Igepal CA630, and a protease inhibitor cocktail consisting of 1 mM phenylmethylsulfonyl fluoride, 0.5 μg/mL leupeptin, pepstatin A, and 2 mM benzamidine. Cells were lysed by freezing and thawing, followed by sonication. Cell debris was removed by centrifugation at 12,000×g for 30 min. The supernatant was further clarified by passing through a 0.45-μm filter (Corning) and then loaded onto a HiTrap chelating column charged with NiSO₄ (Amersham Pharmacia Biotech). The bound protein was eluted with an imidazole solution in a 100-to-500 mM linear gradient. Selected fractions were run through Ni²⁺ column chromatography and were analyzed on a 10% sodium dodecyl sulfate (SDS)-polyacrylamide gel. The purified protein was resolved by electrophoresis in a 12% SDS-PAGE gel and then transferred onto a nitrocellulose membrane. The protein was analyzed by Western blot analysis using monoclonal antibodies against NS3. Proteins were visualized by using a chemiluminescence kit (Roche) with horseradish peroxidase-conjugated goat anti-mouse antibodies (Pierce) as secondary antibodies. The protein was aliquoted and stored at −80° C.

Example 8 Cloning and Expression of HCV Protease A156S, A156T, D168A, D168V Drug-Resistance Mutants and C159S Variant

The mutant DNA fragments of NS4A/NS3 were generated by PCR and cloned into pET expression vector. After transformation into BL21 competent cells, the expression was induced with IPTG for 2 hours. The His-tagged fusion proteins were purified using affinity column followed by size exclusion chromatography.

Example 9

Assay buffer: 2% CHAPS, 50 mM Tris pH 7.5, 50% glycerol, 2 uM M-2235 (Bachem) substrate. In a 50 ul reaction, add 49 ul assay buffer, 1 ul (1U) HCV serine protease (Bioenza). Incubate 20 minutes at room temperature. The plate was read at either 350/460 nm (excitation/emission) on a fluorescent micro-plate reader or monitored at one-minute intervals to achieve the kinetic curve.

The enzyme tolerated 1% DMSO and 2% methanol. In the experiments of testing compounds, the compounds in pure DMSO were diluted 10 times with 20% methanol (10% DMSO and 20% methanol). This compound solution was added to the reaction (not exceeding 10% of the final reaction volume). The final concentration of the organic solvents was: 1% DMSO and 2% methanol.

Example 10 Additional Assay Protocols

Method A:

The compounds were assayed to evaluate the antiviral activity and cytotoxicity of compounds in vitro using HCV RNA replicons. This assay used the cell line ET (luc-ubi-neo/ET), which is a human Huh7 hepatoma cell line that contains an HCV RNA replicon with a stable luciferase (Luc) reporter and three cell culture-adaptive mutations. The HCV RNA levels were directly measured by viral specific TaqMan RT-PCR:

Forward primer: (SEQ ID NO: 63) ACGCAGAAAGCGTCTAGCCAT Reverse primer: (SEQ ID NO: 64) TACTCACCGGTTCCGCAGA Probe: (SEQ ID NO: 65) [6-FAM]-CCTGGAGGCTGCACGACACTCAT-[TAMRA]

The ET cell line was grown in Dulbecco's modified essential media (DMEM), 10% fetal bovine serum (FBS), 1% penicillin-streptomycin (pen-strep), 1% glutamine, 250 μg/mL G418 in a 5% CO₂ incubator at 37° C. All cell culture reagents were obtained from Mediatech (Manassas, Va.). Cells were trypsinized (1% trypsin:EDTA) and plated out at 5×10³ cells/well in white 96-well assay plates (Costar) dedicated to cell number (cytotoxicity) or antiviral activity assessments. Drugs were added at six 3-fold concentrations each and the assay was run in DMEM, 5% FBS, 1% pen-strep, 1% glutamine. Human interferon alpha-2b (PBL Biolabs, New Brunswick, N.J.) was included in each run as a positive control compound. Cells were processed 72 hr post drug addition when the cells are still subconfluent. Antiviral activity was measured by analyzing replicon-derived luciferase activity using the Steady-Glo Luciferase Assay System (Promega, Madison, Wis.) according to manufacturer's instruction. The number of cells in each well was determined by CytoTox-1 reagent (Promega). Compound profile was derived by calculating applicable EC₅₀ (effective concentration inhibiting virus replication by 50%), EC₉₀ (effective concentration inhibiting virus replication by 90%), IC₅₀ (concentration decreasing cell viability by 50%) and SI₅₀ (selective index: EC₅₀/IC₅₀) values. IC₅₀ values for selected compounds are set forth in Table 5, below.

Method B: HCV Protease Assay Using FRET Methodology

A quantitative, fluorescence resonance energy transfer (FRET)-based methodology was employed to identify HCV NS3/4A protease inhibitors. The assay employed a synthetic FRET peptide, derived from the HCV NS5A/5B cleavage site, with the HCV protease to evaluate the activity of compounds against the protease by monitoring the cleavage activity of the complex. A synthetic peptide which encompasses the NS5A-5B junction (NH2-EDVVCCSMSYK-COOH) (SEQ ID NO: 78) was labeled with Dabcyl and Edans at N- and C-termini, respectively (Invitrogen, Carlsbad, Calif.). Fluorescence measurement was used to estimate the IC₅₀ value of the test compound. The two fluorophores form a quenching pair and exhibit FRET within the intact peptide. Upon cleavage of the FRET peptide by HCV NS3/4A proteinase complex (100 ng/mL), the fluorescence is recovered and can be continuously monitored at excitation/emission=340/490 nm.

Example 11 HCV Protease FRET Assay for Mutated NS3/4a 1b Enzymes

The following protocol was used to generate IC₅₀ values as depicted for compounds in Tables 4b and 5. The protocol is a modified FRET-based assay (v_02) from In Vitro Resistance Studies of HCV Serine Protease Inhibitors, 2004, JBC, vol. 279, No. 17, pp 17508-17514. Inherent potency of compounds was assessed against A156S, A156T, D168A, and D168V mutants of the HCV NS3/4A 1b protease enzyme as follows:

10× stocks of NS3/4A protease enzyme from Bioenza (Mountain View, Calif.) and 1.13× 5-FAM/QXL™520 FRET peptide substrate from Anaspec (San Jose, Calif.) were prepared in 50 mM HEPES, pH 7.8, 100 mM NaCl, 5 mM DTT and 20% glycerol. 5 μL of each enzyme were pre-incubated in a Corning (#3573) 384-well, black, non-treated microtiter plate (Corning, N.Y.) for 30 min at 25° C. with a 0.5 μL volume of 50% DMSO and serially diluted compounds prepared in 50% DMSO. Protease reactions were started with the addition of 45 μL of the FRET substrate and monitored for 120 minutes at λ_(ex)487/λ_(em)514 through Quad monochromoters in a Synergy⁴ plate reader from BioTek (Winooski, Vt.). At the conclusion of each assay, progress curves from each well were examined for linear reaction kinetics and fit statistics (R², absolute sum of squares). Initial velocity (0 minutes to 30+ minutes) from each reaction was determined from the slope of a plot of relative fluorescence units vs time (minutes) and then plotted against inhibitor concentration to estimate IC₅₀ from log [Inhibitor] vs Response, Variable Slope model in GraphPad Prism from GraphPad Software (San Diego, Calif.). IC₅₀ values for selected compounds are set forth in Table 5, below.

TABLE 5 Enzymatic Data for Exemplary Compounds (IC₅₀) Compound tested Enzyme/Assay IC₅₀ (nM)¹ (I-1) WT 290 HCV D168A 312 HCV R155K 928 HCV C159S 1090 (I-6) WT 53 HCV D168A 25 (I-11) WT 232 D168A 98 ¹Values greater than one were rounded to the nearest whole number.

Example 12 HCV Protease FRET Assay for WT and Mutated NS3/4A 1b Enzymes (IC₅₀ _(_) _(APP))

The following protocol was used to generate “apparent” IC₅₀ (IC₅₀ _(_) _(APP)) values as depicted in Table 6, below. Without wishing to be bound by any particular theory, it is believed that IC₅₀ _(_) _(APP), constrasted with IC₅₀ values, may provide a more useful indication of time-dependent inhibition, and are thus more representative of binding affinity. The protocol is a modified FRET-based assay (v_03) developed to evaluate compound potency, rank-order and resistance profiles against wild type and C159S, A156S, A156T, D168A, D168V, R155K mutants of the HCV NS3/4A 1b protease enzyme as follows: 10× stocks of NS3/4A protease enzyme from Bioenza (Mountain View, Calif.) and 1.13× 5-FAM/QXL™520 FRET peptide substrate from Anaspec (San Jose, Calif.) were prepared in 50 mM Tris-HCl, pH 7.5, 5 mM DTT, 2% CHAPS and 20% glycerol. 5 μL of each enzyme were added to Corning (#3575) 384-well, black, microtiter plates (Corning, N.Y.) after spotting a 0.5 μL volume of 50% DMSO and serially diluted compounds prepared in 50% DMSO. Protease reactions were immediately started after enzyme addition with the addition of 45 μL of the FRET substrate and monitored for 60-90 minutes at λ_(ex)485/λ_(em)520 in a Synergy⁴ plate reader from BioTek (Winooski, Vt.). At the conclusion of each assay, progress curves from each well were examined for linear reaction kinetics and fit statistics (R², 95% confidence intervals, absolute sum of squares). Initial velocity (0 minutes to 15+ minutes) from each reaction was determined from the slope of a plot of relative fluorescence units vs time (minutes) and then plotted against inhibitor concentration as a percent of the no inhibitor and no enzyme controls to estimate apparent IC₅₀ from log [Inhibitor] vs Response, Variable Slope model in GraphPad Prism from GraphPad Software (San Diego, Calif.).

TABLE 6 Enzymatic Data for Exemplary Compounds Compound tested Enzyme/Assay IC₅₀ _(—) _(APP) (nM)¹ (I-1) WT 1330 HCV A156S >3000 HCV D168A 2550 HCV R155K >3000 HCV C159S >3000 (I-6) WT 456 HCV A156S >3000 HCV D168A 321 HCV R155K 1050 HCV C159S 2070 (I-11) WT 1740 HCV A156S >3000 HCV D168A 1150 HCV R155K >3000 HCV C159S >3000 (I-23) WT >111 HCV A156S 412 HCV A156T 985 HCV D168A 508 HCV D168V 463 ¹Values greater than one were rounded to the nearest whole number.

Example 13

Mass spectrometric analysis of HCV wild type or HCV variant C159S in the presence of test compound is performed. 100 pmols of HCV wild type (Bioenza CA) is incubated with test compound for 1 hr and 3 hrs at 10-fold access of test compound to protein. 1 ul aliquots of the samples (total volume of 4.24 ul) are diluted with 10 ul of 0.1% TFA prior to micro C4 ZipTipping directly onto the MALDI target using Sinapinic acid as the desorption matrix (10 mg/mL in 0.1% TFA:Acetonitrile 50:50). Analyses are performed on a Shimadzu Biotech Axima TOF² (Shimadzu Instruments) matrix-assisted-laser desorption/ionization Time-of-Flight (MALDI-TOF) mass spectrometer. The same procedure is carried out on 100 pmols of HCV C159S mutant of HCV protease for 3 hrs at 10-fold excess of test compound to protein.

Example 14 Modification of Cys159 of Wild-Type HCV Protease Using a Tryptic Digest Strategy

HCV is incubated with test compound for 3 hrs prior to tryptic digestion. Iodoacetamide is used as the alkylating agent after compound incubation. For tryptic digests a 2 ul aliquot (0.06 ug/ul) is diluted with 10 ul of 0.1% TFA prior to micro C18 Zip Tipping directly onto the MALDI target using alpha cyano-4-hydroxy cinnamic acid as the matrix (5 mg/mL in 0.1% TFA:Acetonitrile 50:50).

For tryptic digests the instrument is set in Reflectron mode with a pulsed extraction setting of 1800. Calibration is done using the Laser Biolabs Pep Mix standard (1046.54, 1296.69, 1672.92, 2093.09, 2465.20). For CID/PSD analysis the peptide is selected using cursors to set ion gate timing and fragmentation occurred at a laser power about 20% higher and He is used as the collision gas for CID. Calibration for fragments is done using the P14R fragmentation calibration for the Curved field Reflectron.

Example 15

As depicted in FIGS. 1 and 3, mass spectrometric analysis of HCV wild type in the presence of compounds I-1 and telaprevir was performed using the following protocol: HCV NS3/4A wild type (wt) was incubated for 1 hr at a 10× fold access of test compound to protein. 2 ul aliquots of the samples were diluted with 10 ul of 0.1% TFA prior to micro C4 ZipTipping directly onto the MALDI target using Sinapinic acid as the desorption matrix (10 mg/ml in 0.1% TFA:Acetonitrile 50:50). For intact protein mass measurement the instrument was set in linear mode using a pulsed extraction setting of 24,500 and apomyoglobin as the standard to calibrate the instrument.

As depicted in FIG. 1 (upper panel), compared to the protein with no compound, the protein incubated with compound I-1 has reacted significantly to produce a new species at MW 25,004 Da, which is approximately 537 Da heavier and consistent with the mass of compound I-1 at 547 Da. The lower panel shows no modification of the C159S mutant (see Example 13).

As depicted in FIG. 3, after 1 hour incubation there was no reaction between the protein and telaprevir.

Example 16

As depicted in FIG. 2, mass spectrometric analysis of HCV wild type in the presence of compound I-11 was performed using the following protocol: HCV NS3/4A wild type (wt) was incubated for 3 hr at a 10× fold access of test compound to protein. 2 ul aliquots of the samples were diluted with 10 ul of 0.1% TFA prior to micro C18 ZipTipping directly onto the MALDI target using Sinapinic acid as the desorption matrix (10 mg/ml in 0.1% TFA:Acetonitrile 20:80). For intact protein mass measurement the instrument was set in linear mode using a pulsed extraction setting of 24,500 and apomyoglobin as the standard to calibrate the instrument.

As depicted in FIG. 2, compared to the protein with no compound, the protein incubated with compound I-11 has reacted significantly to produce a new species at MW 25,155 Da, which is approximately 703 Da heavier and consistent with the mass of compound I-11 at 707 Da.

Example 17 Cell Culture

Huh-luc/neo-ET, Huh7-Lunet were obtained from ReBLikon Gmbh (Heidelberg, Germany). Cells were grown in Dulbecco modified Eagle medium (DMEM; Invitrogen) supplemented with 2 mM L-glutamine, nonessential amino acids, 100 U of penicillin/ml, 100 μg of streptomycin/mL, and 10% fetal bovine serum. G418 (Geneticin; Invitrogen) was added at a final concentration of 400 ug/mL. Huh7-Lunet were grown in the absence of G418.

Example 18 Mutant Constructs

Constructs containing clinically relevant mutations were generated by performing site-directed mutagenesis on the pFK-I389-luc-ubi-neo-NS3-3′ET plasmid (ReBLikon Gmbh (Heidelberg, Germany)). using the QuickChange II Site-Directed Mutagenesis Kit (Stratagene, La Jolla, Calif.) according to manufacturer's directions and with the primers described in Table 7, below.

TABLE 7 Primer sequence used to establish Mutant Replicon cell lines. NS3-A156S-F GCTGTGGGCATCTTTCGGTCTGCCGTGTGCACCCGAGGG SEQ ID NO: 66 NS3-A156S-R CCCTCGGGTGCACACGGCAGACCGAAAGATGCCCACAGC SEQ ID NO: 67 NS3-A156T-F GCTGTGGGCATCTTTCGGACTGCCGTGTGCACCCGAGGG SEQ ID NO: 68 NS3-A156T-R CCCTCGGGTGCACACGGCAGTCCGAAAGATGCCCACAGC SEQ ID NO: 69 NS3-D168A-F GGGGTTGCGAAGGCGGTGGCCTTTGTACCCGTCGAGTCT SEQ ID NO: 70 NS3-D168A-R AGACTCGACGGGTACAAAGGCCACCGCCTTCGCAACCCC SEQ ID NO: 71 NS3-D168V-F GGGGTTGCGAAGGCGGTGGTCTTTGTACCCGTCGAGTCT SEQ ID NO: 72 NS3-D168V-R AGACTCGACGGGTACAAAGACCACCGCCTTCGCAACCCC SEQ ID NO: 73 NS3-C159S-F ATCTTTCGGGCTGCCGTGAGCACCCGAGGGGTTGCGAAG SEQ ID NO: 74 NS3-C159S-R CTTCGCAACCCCTCGGGTGCTCACGGCAGCCCGAAAGAT SEQ ID NO: 75 NS3-R155K-F CACGCTGTGGGCATCTTTAAGGCTGCCGTGTGCACCCGA SEQ ID NO: 76 NS3-R155K-R TCGGGTGCACACGGCAGCCTTAAAGATGCCCACAGCGTG SEQ ID NO: 77

Example 19 In Vitro Transcription

In vitro transcripts of HCV positive strands were generated by using the protocol described by Lohmann V et al., J. Virol., 77:3007-3019, 2003. For transcription of positive-strand HCV RNAs, plasmid DNA (pFK 1341 PI-Luc/NS3-3′/ET, obtained from ReBLikon Gmbh (Heidelberg, Germany)), was digested with AseI followed by Sca1. After restriction digest, DNA was extracted with phenol and chloroform, precipitated with ethanol, and dissolved in RNase-free water. In vitro transcription reactions contained 80 mM HEPES (pH 7.5), 12 mM MgCl₂, 2 mM spermidine, 40 mM dithiothreitol, a 3.125 mM concentration of each nucleoside triphosphate, 1 U of RNasin. 5 ug of restricted plasmid DNA and 80 U of T7 RNA polymerase (Promega) was used. After 2 h at 37° C., an additional 40 U of T7 polymerase was added, and the reaction was incubated for another 2 h. Transcription was terminated by the addition of 1 U of RNase-free DNase (Promega) per ug of plasmid DNA, followed by incubation for 30 min at 37° C. After extraction with acidic phenol and chloroform, RNA was precipitated with isopropanol and dissolved in RNase-free water. The concentration was determined by measurement of the optical density at 260 nm (OD260), and RNA integrity was checked by denaturing agarose gel electrophoresis.

Example 20 Transfection of HCV Full Length Genome and Selection of Stable Cell Lines

7×10⁴ Huh7-Lunet cells were seeded over night in a 12 well plate, the next day 1 ug of RNA/well was transfected using Minis Tx (Madison, Wis.) kit. Transfection was performed according to manufacturer's instructions, and 24 hours after transfection cells were either subjected to Luciferase assay or subjected to G418 (400 ug/ml) selection in order to establish stable cell lines.

Example 21 Luciferase Assay

The compounds are assayed to evaluate the antiviral activity and cytotoxicity of compounds using replicon-derived luciferase activity. This assay uses the cell line ET (luc-ubi-neo/ET), which is a human Huh7 hepatoma cell line that contains an HCV RNA replicon with a stable luciferase (Luc) reporter and cell culture-adaptive mutations. The ET cell line is grown in a 5% CO₂ incubator at 37° C. in Dulbecco's modified essential media (DMEM) supplemented with 2 mM L-glutamine, nonessential amino acids, 100 U of penicillin/ml, 100 μg of streptomycin/mL, and 10% fetal bovine serum. G418 (Geneticin; Invitrogen) is added at a final concentration of 400 ug/mL.

All cell culture reagents are obtained from Invitrogen (Carlsbad). Cells are trypsinized (1% trypsin:EDTA) and plated out at 5×10³ cells/well in white 96-well assay plates (Costar) dedicated to cell number (cytotoxicity) or antiviral activity assessments. Test compounds are added at six 3-fold concentrations each and the assay is run in DMEM, 5% FBS, 1% pen-strep, 1% glutamine, 1% non essential amino acid. Human interferon alpha-2b (PBL Biolabs, New Brunswick, N.J.) is included in each run as a positive control compound. Cells are processed 72 hr post test compound addition when the cells are still subconfluent. Antiviral activity is measured by analyzing replicon-derived luciferase activity using the Steady-Glo Luciferase Assay System (Promega, Madison, Wis.) according to manufacturer's instruction. The number of cells in each well is determined by Cell Titer Blue Assay (Promega). Compound profile is derived by calculating applicable EC₅₀ (effective concentration inhibiting virus replication by 50%), EC₉₀ (effective concentration inhibiting virus replication by 90%), IC₅₀ (concentration decreasing cell viability by 50%) and SI₅₀ (selective index: EC₅₀/IC₅₀) values.

While we have described a number of embodiments of this invention, it is apparent that our basic examples may be altered to provide other embodiments that utilize the compounds and methods of this invention. Therefore, it will be appreciated that the scope of this invention is to be defined by the appended claims rather than by the specific embodiments that have been represented by way of example. 

We claim:
 1. A conjugate of the formula Cys159-linker-inhibitor moiety, wherein the Cys159 is Cys159 of HCV protease, wherein the inhibitor moiety is of formula A:

or a pharmaceutically acceptable salt thereof, wherein: one of R^(a) and R^(b) is hydrogen and the other is —OH or —OC(O)R′, or R^(a) and R^(b) are taken together to form an oxo group; R′ is an optionally substituted group selected from C₁₋₆ aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R¹ is an optionally substituted group selected from C₁₋₆ aliphatic or C₃₋₇ cycloalkyl(C₁₋₃ alkyl); R² is hydrogen or an optionally substituted group selected from C₁₋₆ aliphatic or C₃₋₇ cycloalkyl; R^(x) and R^(y) are taken together to form an optionally substituted C₃₋₇ membered ring having 0-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R⁴ is —NHC(O)NHR⁵, —NHC(O)OR⁶, or

R⁵ is an optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R⁶ is an optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; R⁷ is an optionally substituted group selected from C₁₋₆ aliphatic, bridged bicyclic, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur; and R is hydrogen or an optionally substituted group selected from C₁₋₆ aliphatic, C₃₋₇ cycloalkyl, 6-10 membered aryl, 5-10 membered heteroaryl having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur, or 4-7 membered heterocyclyl having 1-2 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
 2. The conjugate of claim 1, wherein R¹ is n-propyl.
 3. The conjugate of claim 1, wherein R¹ is


4. The conjugate of claim 1, wherein R² is cyclopropyl.
 5. The conjugate of claim 1, wherein R⁴ is —NHC(O)OR⁶.
 6. The conjugate of claim 1, wherein R⁵ is an optionally substituted 5-10 membered heteroaryl group having 1-4 heteroatoms independently selected from nitrogen, oxygen, or sulfur.
 7. The conjugate of claim 6, wherein R⁵ is


8. The conjugate of claim 1, wherein R⁵ is an optionally substituted C₁₋₆ aliphatic group.
 9. The conjugate of claim 8, wherein R⁵ is t-butyl.
 10. The conjugate of claim 1, wherein R⁷ is an optionally substituted C₃₋₇ cycloalkyl group.
 11. The conjugate of claim 10, wherein R⁷ is cyclohexyl.
 12. The conjugate of claim 1, wherein the linker is a bivalent group derived from the reaction of a warhead group —(CH₂)_(n)-L-Y with the Cys159 of HCV protease, wherein: n is an integer from 0 to 5, inclusive; L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and one or two additional methylene units of L are optionally and independently replaced by —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, —C(O)O—, cyclopropylene, —O—, —N(R)—, or —C(O)—; Y is hydrogen, C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN, or a 3-10 membered monocyclic or bicyclic, saturated, partially unsaturated, or aryl ring having 0-3 heteroatoms independently selected from nitrogen, oxygen, or sulfur, and wherein said ring is substituted with 1-4 R^(e) groups; and each R^(e) is independently selected from -Q-Z, oxo, NO₂, halogen, CN, a suitable leaving group, or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN, wherein: Q is a covalent bond or a bivalent C₁₋₆ saturated or unsaturated, straight or branched, hydrocarbon chain, wherein one or two methylene units of Q are optionally and independently replaced by —N(R)—, —S—, —O—, —C(O)—, —OC(O)—, —C(O)O—, —SO—, or —SO₂—, —N(R)C(O)—, —C(O)N(R)—, —N(R)SO₂—, or —SO₂N(R)—; and Z is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN.
 13. The conjugate according to claim 12, wherein n is an integer from 1 to 5, inclusive.
 14. The conjugate according to claim 12, wherein: L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—; and Y is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN.
 15. The conjugate according to claim 14, wherein L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —C(O)—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—.
 16. The conjugate according to claim 14, wherein L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one double bond and at least one methylene unit of L is replaced by —OC(O)—.
 17. The conjugate according to claim 12, wherein L is —NRC(O)CH═CH—, —NRC(O)CH═CHCH₂N(CH₃)—, —NRSO₂CH═CH—, —NRSO₂CH═CHCH₂—, —NRC(O)CH═CHCH₂O—, —NRC(O)C(═CH₂)CH₂—, or —CH₂NRC(O)CH═CH—; wherein the R group of L is H or optionally substituted C₁₋₆ aliphatic; and Y is hydrogen or C₁₋₆ aliphatic optionally substituted with oxo, halogen, NO₂, or CN.
 18. The conjugate according to claim 17, wherein L is —NHC(O)CH═CH—, —NHC(O)CH═CHCH₂N(CH₃)—, —NHSO₂CH═CH—, —NHSO₂CH═CHCH₂—, —NHC(O)CH═CHCH₂O—, —NHC(O)C(═CH₂)CH₂—, or —CH₂NHC(O)CH═CH—.
 19. The conjugate according to claim 12, wherein L is a bivalent C₂₋₈ straight or branched, hydrocarbon chain wherein L has at least one alkylidenyl double bond and at least one methylene unit of L is replaced by —C(O)—, —NRC(O)—, —C(O)NR—, —N(R)SO₂—, —SO₂N(R)—, —S—, —S(O)—, —SO₂—, —OC(O)—, or —C(O)O—, and one additional methylene unit of L is optionally replaced by cyclopropylene, —O—, —N(R)—, or —C(O)—. 